Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine

Yang, Changwon,Kim, Eunae,Lim, Manho,Pak, Youngshang American Chemical Society 2019 Journal of chemical theory and computation Vol.15 No.1

<P>DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 μs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.</P> [FIG OMISSION]</BR>

Palmitic acid induces inflammatory cytokines and regulates tRNA-derived stress-induced RNAs in human trophoblasts

Changwon Yang,Garam An,Jisoo Song,Gwonhwa Song,Whasun Lim The Korean Society of Animal Reproduction and Biot 2022 한국동물생명공학회지 Vol.37 No.4

High levels of proinflammatory cytokines have been observed in obese pregnancies. Obesity during pregnancy may increase the risk of various pregnancyrelated complications, with pathogenesis resulting from excessive inflammation. Palmitic acid (PA) is a saturated fatty acid that circulates in high levels in obese women. In our previous study, we found that PA inhibited the proliferation of trophoblasts developing into the placenta, induced apoptosis, and regulated the number of cleaved halves derived from transfer RNAs (tRNAs). However, it is not known how the expression of tRNA-derived stress-induced RNAs (tiRNAs) changes in response to PA treatment at concentrations that induce inflammation in human trophoblasts. We selected concentrations that did not affect cell viability after dose-dependent treatment of HTR8/SVneo cells, a human trophoblast cell line. PA (200 μM) did not affect the expression of apoptotic proteins in HTR8/SVneo cells. PA significantly increased the expression of inflammatory cytokines including interleukin (IL)-1β, IL-6, IL-8, and tumor necrosis factor (TNF)-α. In addition, 200 μM PA significantly increased the expression of tiRNAs compared to 800 μM PA treatment. These results suggest that PA impairs placental development during early pregnancy by inducing an inflammatory response in human trophoblasts. In addition, this study provides a basis for further research on the association between PA-induced inflammation and tiRNA generation.

Luteolin Suppresses Proliferation of Choriocarcinoma Cells through Regulating PI3K/AKT Signaling Pathway and Blocking Transcriptional Activity of SREBP1

Changwon Yang,Whasun Lim,Gwonhwa Song 한국식품영양과학회 2016 한국식품영양과학회 학술대회발표집 Vol.2016 No.10

Homosalate aggravates the invasion of human trophoblast cells as well as regulates intracellular signaling pathways including PI3K/AKT and MAPK pathways

Yang, Changwon,Lim, Whasun,Bazer, Fuller W.,Song, Gwonhwa Elsevier 2018 Environmental pollution Vol.243 No.2

<P><B>Abstract</B></P> <P>Homosalate is an organic ultraviolet filter used in most sunscreens but has been reported to be toxic to marine organisms. The estrogenic activity of homosalate has also been reported, but its endocrine-disrupting effect remains unclear. Although homosalate has been detected in human placental tissues, its effect on the survival of human trophoblast cells needs to be investigated. Therefore, in this study, we evaluated if HTR8/SVneo, a human trophoblast cell line, treated with homosalate showed decreasing proliferative activity in a dose-dependent manner. Homosalate promoted the death of HTR8/SVneo cells with elevated lipid peroxidation and intracellular Ca<SUP>2+</SUP> concentration. It also induced endoplasmic reticulum stress and mitochondrial morphological disturbances associated with the differentiation of human trophoblast cells. However, when the intracellular Ca<SUP>2+</SUP> or reactive oxygen species were removed using BAPTA-AM or N-acetyl-L-cysteine (NAC), the cell proliferation suppressed by homosalate was restored. Homosalate also significantly inhibited the invasion of HTR8/SVneo cells. Furthermore, it modulated phosphoinositide 3-kinase (PI3K)/AKT and mitogen-activated protein kinase (MAPK) signaling pathways, which were involved in the cross-talk between both signaling pathways in HTR8/SVneo cells. Thus, homosalate adversely affects the survival, proliferation, and invasiveness of human trophoblast cells and therefore pregnant women should practice caution while using personal care products containing homosalate.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Homosalate inhibits survival and proliferation and invasion of human trophoblasts. </LI> <LI> Homosalate blocks AKT and MAPK signaling pathways in trophoblast cells. </LI> <LI> Homosalate-induced oxidative stress results in disruption of mitochondrial membrane. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>A schematic diagram illustrating current working hypothesis regarding the effects of homosalate on human trophoblast cells. Homosalate induces ROS production in human trophoblast cells, followed by excessive lipid peroxidation. Furthermore, elevated ROS increases cytosolic Ca<SUP>2+</SUP> concentration accompanied by loss of mitochondrial membrane potential (MMP). The disruption of mitochondrial membrane causes apoptotic cell death of human trophoblast cells. Moreover, homosalate activates phosphorylation of PI3K/AKT pathways and MAPK pathways with cross-talk between the two pathways. Finally, the alteration of signaling pathways causes transcriptional regulation in nucleus, leading to downregulation of proliferation and invasion of human trophoblast cells.</P> <P>[DISPLAY OMISSION]</P>

Probing α/β Balances in Modified Amber Force Fields from a Molecular Dynamics Study on a ββα Model Protein (1FSD)

Yang, Changwon,Kim, Eunae,Pak, Youngshang Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.6

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin

Yang, Changwon,Kim, Eunae,Pak, Youngshang Korean Chemical Society 2012 Bulletin of the Korean Chemical Society Vol.33 No.11

Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specifically binds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling molecular dynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pulling the DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energy cost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial binding affinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate. Possible structural changes of this complex in the plateau were investigated in details.

Quercetin Affects Spermatogenesis-Related Genes of Mouse Exposed to High-Cholesterol Diet

Changwon Yang,Hyocheol Bae,Gwonhwa Song,Whasun Lim 한국동물생명공학회(구 한국동물번식학회) 2020 Journal of Animal Reproduction and Biotechnology Vol.35 No.1

A high-cholesterol diet can reduce male fertility. However, it is not known whether a high-cholesterol diet can regulate the expression of genes involved in sperm maturation and sperm fertilizing ability. Quercetin, a natural product, is known to have cytoprotective effects by regulating lipid metabolism in various cell types. This study aimed to confirm the expression of genes involved in sperm maturation in the testes of mice fed a high-cholesterol diet and to determine whether quercetin can reverse the genetic regulation of cholesterol. Mice were divided into groups fed a normal chow diet and a high-cholesterol diet. Mice fed the high-cholesterol diet were dose-dependently supplemented with quercetin for 6 weeks. Investigations using quantitative PCR and in situ hybridization revealed that the high-cholesterol diet alters the expression of genes associated with sperm maturation in the testes of mice, and this was reversed with the supplementation of quercetin. In addition, the high-cholesterol diet regulated the expression of genes related to lipid metabolism in the liver of mice. Under a high-cholesterol diet, quercetin can improve male fertility by regulating the expression of genes involved in sperm maturation.

<i>In</i> <i>silico</i> direct folding of thrombin-binding aptamer G-quadruplex at all-atom level

Yang, Changwon,Kulkarni, Mandar,Lim, Manho,Pak, Youngshang Oxford University Press 2017 Nucleic acids research Vol.45 No.22

<P><B>Abstract</B></P><P>The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K<SUP>+</SUP>-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K<SUP>+</SUP> ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers.</P>

Decanoic acid suppresses proliferation and invasiveness of human trophoblast cells by disrupting mitochondrial function

Yang, Changwon,Lim, Whasun,Bazer, Fuller W.,Song, Gwonhwa Elsevier 2018 Toxicology and applied pharmacology Vol.339 No.-

<P><B>Abstract</B></P> <P>Decanoic acid (DA) is a medium-chain fatty acid used in the manufacture of various products including plastics, cosmetics, and lubricants. In addition to antiviral and antibacterial effects, DA's, reported biological activities include regulation of signaling pathways and redox homeostasis in various human cell types. The influence of DA on functional properties of human trophoblasts, including proliferation, invasion and apoptosis is currently unknown. In the present study, we evaluated the anti-proliferative and anti-invasive effects of DA on the human trophoblast cell line HTR8/SVneo. In addition, DA induced oxidative stress, as evidenced by generation of reactive oxygen species (ROS) and induction of lipid peroxidation (LPO). This oxidative stress was accompanied by activation of the mitochondria-dependent apoptotic pathway in HTR8/SVneo cells. We also observed elevated mitochondrial Ca<SUP>2+</SUP>, and loss of mitochondrial membrane potential in response to DA treatment. Chelation of mitochondrial Ca<SUP>2+</SUP> using BAPTA-AM rescued cellular proliferation suppressed by DA. We also verified that signaling proteins including AKT, P70S6K, S6, and ERK1/2 and their targets were significantly reduced in HTR8/SVneo cells by DA treatment. Pre-treatment of cells with selective inhibitors of AKT (LY294002) and ERK1/2 (U0126) revealed that the AKT and ERK1/2 signaling pathways regulated by DA displayed cross-talk in HTR8/SVneo cells. Collectively, these results suggest that personal products containing DA will have harmful effects on human trophoblasts, and could cause implantation and placentation failure during early pregnancy.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Decanoic acid inhibits proliferation and invasion of human trophoblasts. </LI> <LI> Decanoic acid blocks AKT and ERK1/2 signaling pathways in human trophoblasts. </LI> <LI> Decanoic acid-induced oxidative stress results in mitochondrial membrane disruption. </LI> </UL> </P>

Quercetin Affects Spermatogenesis-Related Genes of Mouse Exposed to High-Cholesterol Diet

Yang, Changwon,Bae, Hyocheol,Song, Gwonhwa,Lim, Whasun The Korean Society of Animal Reproduction and Biot 2020 한국동물생명공학회지 Vol.35 No.1

A high-cholesterol diet can reduce male fertility. However, it is not known whether a high-cholesterol diet can regulate the expression of genes involved in sperm maturation and sperm fertilizing ability. Quercetin, a natural product, is known to have cytoprotective effects by regulating lipid metabolism in various cell types. This study aimed to confirm the expression of genes involved in sperm maturation in the testes of mice fed a high-cholesterol diet and to determine whether quercetin can reverse the genetic regulation of cholesterol. Mice were divided into groups fed a normal chow diet and a high-cholesterol diet. Mice fed the high-cholesterol diet were dose-dependently supplemented with quercetin for 6 weeks. Investigations using quantitative PCR and in situ hybridization revealed that the high-cholesterol diet alters the expression of genes associated with sperm maturation in the testes of mice, and this was reversed with the supplementation of quercetin. In addition, the high-cholesterol diet regulated the expression of genes related to lipid metabolism in the liver of mice. Under a high-cholesterol diet, quercetin can improve male fertility by regulating the expression of genes involved in sperm maturation.