scholarly journals Effect of Copper(II) Ion Binding by Porin P1 Precursor Fragments from Fusobacterium nucleatum on DNA Degradation

2021 ◽  
Vol 22 (22) ◽  
pp. 12541
Author(s):  
Kamila Stokowa-Sołtys ◽  
Kamil Wojtkowiak ◽  
Valentyn Dzyhovskyi ◽  
Robert Wieczorek
Keyword(s):  
Dna Cleavage ◽  
Density Functional ◽  
Outer Membrane Proteins ◽  
Fusobacterium Nucleatum ◽  
Dna Degradation ◽  
Ros Generation ◽  
Oxygen Donor ◽  
Hydrogen Bond Networks ◽  
Dna Strands ◽  
Effect Of Copper

Fusobacterium nucleatum is one of the most notorious species involved in colorectal cancer. It was reported that numerous outer membrane proteins (OMP) are actively involved in carcinogenesis. In this paper, the structure and stability of certain complexes, as well as DNA cleavage and ROS generation by fragments of OMP, were investigated using experimental and theoretical methods. Mass spectrometry, potentiometry, UV-Vis, CD, EPR, gel electrophoresis and calculations at the density functional theory (DFT) level were applied. Two consecutive model peptides, Ac-AKGHEHQLE-NH2 and Ac-FGEHEHGRD-NH2, were studied. Both of these were rendered to form a variety of thermodynamically stable complexes with copper(II) ions. All of the complexes were stabilized, mainly due to interactions of metal with nitrogen and oxygen donor atoms, as well as rich hydrogen bond networks. It was also concluded that these complexes in the presence of hydrogen peroxide or ascorbic acid can effectively produce hydroxyl radicals and have an ability to cleave the DNA strands. Surprisingly, the second studied ligand at the micromolar concentration range causes overall DNA degradation.

scholarly journals Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double Strand

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3986
Author(s):  
Cécilia Hognon ◽  
Antonio Monari
Keyword(s):  
Dna Cleavage ◽  
Catalytic Mechanism ◽  
Dna Lesions ◽  
Cleavage Reaction ◽  
Dynamic Simulations ◽  
Important Target ◽  
System Adaptation ◽  
Dna Strands ◽  
Dna Strand ◽  
Dna Substrate

Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.

scholarly journals Fusobacterium nucleatum Facilitates Apoptosis, ROS Generation, and Inflammatory Cytokine Production by Activating AKT/MAPK and NF-κB Signaling Pathways in Human Gingival Fibroblasts

2019 ◽  
Vol 2019 ◽  
pp. 1-22 ◽  
Author(s):  
Wenyan Kang ◽  
Zhilong Jia ◽  
Di Tang ◽  
Zhanwei Zhang ◽  
Hui Gao ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Cell Apoptosis ◽  
Inflammatory Cytokine ◽  
Cytokine Production ◽  
Fusobacterium Nucleatum ◽  
Human Gingival Fibroblasts ◽  
Ros Generation ◽  
Gingival Fibroblasts ◽  
Inflammatory Cytokine Production ◽  
Pathogenic Effects

Fusobacterium nucleatum (F. nucleatum) plays key roles in the initiation and progression of periodontitis. However, the pathogenic effect of F. nucleatum on human oral tissues and cells has not been fully evaluated. In this study, we aimed to analyze the pathogenic effects of F. nucleatum on human gingival fibroblasts (GFs) and clarify the potential mechanisms. RNA-sequencing analysis confirmed that F. nucleatum significantly altered the gene expression of GF as the stimulation time increased. Cell counting and EdU-labeling assays indicated that F. nucleatum inhibited GF proliferation and promoted cell apoptosis in a time- and dose-dependent manner. In addition, cell apoptosis, intracellular reactive oxygen species (ROS) generation, and proinflammatory cytokine production were dramatically elevated after F. nucleatum stimulation. Furthermore, we found that the AKT/MAPK and NF-κB signaling pathways were significantly activated by F. nucleatum infection and that a large number of genes related to cellular proliferation, apoptosis, ROS, and inflammatory cytokine production downstream of AKT/MAPK and NF-κB signaling pathways were significantly altered in F. nucleatum-stimulated GFs. These findings suggest that F. nucleatum inhibits GF proliferation and promotes cell apoptosis, ROS generation, and inflammatory cytokine production partly by activating the AKT/MAPK and NF-κB signaling pathways. Our study opens a new window for understanding the pathogenic effects of periodontal pathogens on the host oral system.

scholarly journals Requirements for proteolysis during apoptosis.

1997 ◽  
Vol 17 (11) ◽  
pp. 6502-6507 ◽  
Author(s):  
D L Vaux ◽  
S Wilhelm ◽  
G Häcker
Keyword(s):  
Dna Cleavage ◽  
Morphological Changes ◽  
Cysteine Proteases ◽  
Dna Degradation ◽  
Effector Proteins ◽  
Proteinase K ◽  
Caspase Activation ◽  
Caspase Substrate ◽  
Do So

The key effector proteins of apoptosis are a family of cysteine proteases termed caspases. Following activation of caspases, biochemical events occur that lead to DNA degradation and the characteristic morphological changes associated with apoptosis. Here we show that cytoplasmic extracts activated in vitro by proteinase K were able to cleave the caspase substrate DEVD-7-amino-4-methylcoumarin, while neither proteinase K nor nonactivated extracts were able to do so alone. Caspase-like activity was inhibited by the specific caspase inhibitor DEVD-aldehyde and by the protease inhibitor iodoacetamide, but not by N-ethylmaleimide. When added to isolated nuclei, the activated extracts caused internucleosomal DNA degradation and morphological changes typical of apoptosis. As DNA cleavage and morphological changes could be inhibited by N-ethylmaleimide but not by iodoacetamide, we conclude that during apoptosis, caspase activation causes activation of another cytoplasmic enzyme that can be inhibited by N-ethylmaleimide. Activity of this enzyme is necessary for activation of endonucleases, DNA cleavage, and changes in nuclear morphology.

scholarly journals Mechanistic Insights into theCis-andTrans-acting Deoxyribonuclease Activities of Cas12a

2018 ◽  
Author(s):  
Daan C. Swarts ◽  
Martin Jinek
Keyword(s):  
Genome Editing ◽  
Dna Cleavage ◽  
Cleavage Product ◽  
List Type ◽  
Francisella Novicida ◽  
Ssdna Binding ◽  
Double Stranded Dna ◽  
Target Dna ◽  
Dna Strands ◽  
Dna Strand

HIGHLIGHTSTarget ssDNA binding allosterically induces unblocking of the RuvC active sitePAM binding facilitates unwinding of dsDNA targetsNon-target DNA strand cleavage is prerequisite for target DNA strand cleavageAfter DNA cleavage, Cas12a releases the PAM-distal DNA productSUMMARYCRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA incisand non-target single stranded DNAs (ssDNA) intrans.To elucidate the molecular basis for both deoxyribonuclease cleavage modes, we performed structural and biochemical studies onFrancisella novicidaCas12a. We show how crRNA-target DNA strand hybridization conformationally activates Cas12a, triggering itstrans-acting, non-specific, single-stranded deoxyribonuclease activity. In turn,cis-cleavage of double-stranded DNA targets is a result of PAM-dependent DNA duplex unwinding and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent,trans-active state. Together, these results provide a revised model for the molecular mechanism of Cas12a enzymes that explains theircis- andtrans-acting deoxyribonuclease activities, and additionally contribute to improving Cas12a-based genome editing.

scholarly journals Hydrogenated Amorphous TiO2−x and Its High Visible Light Photoactivity

Nanomaterials ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2801
Author(s):  
Guang Feng ◽  
Mengyun Hu ◽  
Shuai Yuan ◽  
Junyi Nan ◽  
Heping Zeng
Keyword(s):  
Methylene Blue ◽  
Visible Light ◽  
Rhodamine B ◽  
Environmental Remediation ◽  
Density Functional ◽  
Electronic Band Structure ◽  
Ros Generation ◽  
Electronic Band ◽  
Amorphous Tio2 ◽  
Hydrogenated Amorphous

Hydrogenated crystalline TiO2 with oxygen vacancy (OV) defect has been broadly investigated in recent years. Different from crystalline TiO2, hydrogenated amorphous TiO2−x for advanced photocatalytic applications is scarcely reported. In this work, we prepared hydrogenated amorphous TiO2−x (HA-TiO2−x) using a unique liquid plasma hydrogenation strategy, and demonstrated its highly visible-light photoactivity. Density functional theory combined with comprehensive analyses was to gain fundamental understanding of the correlation among the OV concentration, electronic band structure, photon capturing, reactive oxygen species (ROS) generation, and photocatalytic activity. One important finding was that the narrower the bandgap HA-TiO2−x possessed, the higher photocatalytic efficiency it exhibited. Given the narrow bandgap and extraordinary visible-light absorption, HA-TiO2−x showed excellent visible-light photodegradation in rhodamine B (98.7%), methylene blue (99.85%), and theophylline (99.87) within two hours, as well as long-term stability. The total organic carbon (TOC) removal rates of rhodamine B, methylene blue, and theophylline were measured to 55%, 61.8%, and 50.7%, respectively, which indicated that HA-TiO2−x exhibited high wastewater purification performance. This study provided a direct and effective hydrogenation method to produce reduced amorphous TiO2−x which has great potential in practical environmental remediation.

scholarly journals Cu-Doped KCl Unfolded Band Structure and Optical Properties Studied by DFT Calculations

2020 ◽  
Author(s):  
Cesar Castillo-Quevedo ◽  
Jose Luis Cabellos ◽  
Raul Aceves ◽  
Roberto Núñez-González ◽  
Alvaro Posada-Amarillas
Keyword(s):  
Optical Properties ◽  
Band Structure ◽  
Density Functional ◽  
Copper Ions ◽  
Point Of View ◽  
Basis Set ◽  
Theoretical Point ◽  
Conduction Bands ◽  
Cu Substitution ◽  
Effect Of Copper

The unfolded band structure and optical properties of Cu-doped KCl crystals were computed by first principles within the framework of density functional theory, implemented in the ABINIT electronic structure package utilizing pseudopotential approximation and a plane-wave basis set. From a theoretical point of view, Cu substitution into pristine KCl crystals requires calculation by the supercell (SC) method. This procedure shrinks the Brillouin zone, resulting in a folded band structure that is difficult to interpret. To solve this problem and gain insight into the effect of copper ions (Cu+) on electronic properties, the band structure of SC KCl:Cu was unfolded to make a direct comparison with the band structure of the primitive cell (PC) of pristine KCl. To understand the effect of Cu substitution on optical absorption, we calculated the imaginary part of the dielectric function of KCl:Cu through a sum-over-states formalism and broke it down into different band contributions by partially making an iterated cumulative sum (ICS) of selected valence and conduction bands. Consequently, we identified those interband transitions that give rise to the absorption peaks due to the Cu+ ion. These transitions involve valence and conduction bands formed by the Cu-3d and Cu-4s electronic states

scholarly journals Outer membrane proteins as major antigens of Fusobacterium nucleatum

1989 ◽  
Vol 47 (8-9) ◽  
pp. 473-484 ◽  
Author(s):  
Vidar Bakken ◽  
Stig Aarø ◽  
Tor Hofstad ◽  
Endre N. Vasstrand
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Fusobacterium Nucleatum

scholarly journals Computational Modeling of the Mechanism of Urease

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Håkan Carlsson ◽  
Ebbe Nordlander
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Hydrolytic Enzyme ◽  
Nickel Atom ◽  
Nickel Ion ◽  
Functional Theory ◽  
Amine Nitrogen ◽  
Tetrahedral Intermediate ◽  
Oxygen Donor

In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).

scholarly journals Design, Synthesis, Characterization and Antiproliferative Activities of Ru(II) Complexes of Substituted Benzimidazoles

2019 ◽  
Vol 31 (10) ◽  
pp. 2311-2318
Author(s):  
Ashok K. Singh ◽  
Snehlata Katheria ◽  
Amrendra Kumar ◽  
Asiff Zafri ◽  
Mohd. Arshad
Keyword(s):  
Cell Death ◽  
Mtt Assay ◽  
Hela Cells ◽  
Density Functional ◽  
Ros Generation ◽  
Spectroscopic Techniques ◽  
Dependent Manner ◽  
Apoptotic Pathway ◽  
Design Synthesis ◽  
Cytotoxicity Effects

Synthesis of [Ru(PPh3)2(BZM)2Cl2] (BZM= LS1, LS2, LS3, LS4 and LS5) where LS1=(1H-benzo[d] imidazole-2-yl)methanethiol, LS2 = 2-(4-bromobutyl)-1H-benzo[d] imidazole, LS3= 2-(4-nitrophenyl)-1H-benzo[d]imidazole, LS4 = 2-(4-chlorophenyl)-1H-benzo[d]imidazole and LS5= 4-(1H-benzo[d]imidazol-2-yl)aniline (BZM = benzimidazoles, PPh3 = triphenylphosphine) and metal complexes as MR, [ Ru (PPh3)4Cl2], MLS1, MLS2, MLS3, MLS4 and MLS5 for use as potential anticancer compounds have been investigated. The complexes have been characterized by elemental analysis, IR, multinuclear NMR, UV-visible and ESI-MS spectroscopic techniques. The geometries of all complexes have been optimized by using density functional theory (DFT). The cytotoxicity effects of MR, MLS2 and LS1 were also investigated on Human cervical carcinoma cells (HeLa) by MTT assay, ROS generation and nuclear apoptosis assay. The percent cell viability assessed by MTT assay suggested that the synthesized MR, MLS2 and LS1 significantly reduce the viability of HeLa cells, in a dose-dependent manner. The inhibitory concentration (IC50) of MR, MLS2 and LS1 against HeLa cells was found 90.8, 81.8 and 115 μM, respectively. These compounds also induced the over production of intracellular reactive oxygen species (ROS) as well as the condensed and fragmented nucleus, which supports the molecular mechanism of cell death by apoptosis. The investigations suggested that the compounds MR, MLS2 and LS1 induce the cell death in HeLa cells through apoptotic pathway.

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