Conformational Changes in DNA and Soft Modes

Abstract

In this paper we explore the applicability of the soft mode approach to study the conformational transitions of DNA. It is believed that the A-B conformation change is a first order transition. Soft mode theories only apply to the initial stages of a first order transition. However the mode softening in such a case can be the initiating factor which ultimately leads to the transition. The first order transition is, then, a breakdown of what otherwise would have been a true second order transition. The mode softening is causally connected to onset of the transition. We use the eigenvectors obtained from lattice dynamics calculations to identify the softmode. We use the eigenvector projections to form a force constimi matrix that is required to drive a mode soft. We explore the methods by which this force constant matrix can be formed. We suggest that the breaking of specific “water bridges” between phosphate groups in the two single strands can drive the conformation change.     

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

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Highlights? Cbf1 and Tye7 are paralogous TFs with virtually identical DNA binding-site motifs ? The two paralogous TFs bind different genomic target sites in vivo ? The genomic context of putative DNA binding sites affects TF binding specificity ? Structural analyses suggest that genomic context influences TF binding through DNA shape     

Stereoselective Accumulation of Propranolol Enantiomers in K562 and K562/ADR Cells

The stereoselective uptake of propranolol enantiomers was investigated by using the K562 and K562 adriamycin‐resistant cell line (K562/ADR) as a model. An enantioselective RP‐HPLC method was applied to determine the accumulation of propranolol (PPL) stereoisomers in K562 and K562/ADR cells. The concentration, time and temperature dependent studies showed that the accumulation of S‐(?)‐PPL was higher than R‐(+)‐PPL in K562 cells and uptake of R‐(+)‐PPL was significantly higher than that of S‐(?)‐PPL in K562/ADR cells. The results indicate the enantioselective accumulation of propranolol enantiomers in K562 and K562 / ADR cells. Chirality 25:361–364, 2013. © 2013 Wiley Periodicals, Inc.     

原子力显微镜观测紫外线诱导的K562肿瘤细胞DNA损伤

利用彗星电泳检测出UVB、UVC短时间照射会使肿瘤细胞的DNA发生断裂,而长时间照射之后彗星电泳无法检测到碎片,推测可能是由于DNA分子交联的原因[1],国内外尚无定论.为了更直观的研究这种现象,提取了UVB,UVA照射后K562细胞的DNA,并调节到合适的浓度在原子力显微镜下观测.实验结果表明UVB对K562肿瘤细胞DNA损伤的影响呈现时间/剂量效应,较短时间照射主要产生DNA的链断裂,较长时间辐射则主要产生DNA链的交联.UVC对K562肿瘤细胞DNA的损伤大于UVB.UVC短时照射即可引起DNA的断裂和交联,较长时间辐射主要产生交联和一些断裂;长时间照射不但产生大量交联,同时有大量断裂产生,并发生凝缩和缠绕等结构破坏.     

Changes in Gene Expression and DNA Methylation of Evolutionarily Young AluY Repeats during Apoptosis of Human K562 Erythro-Myeloblastic Leukemia Cells

Using a human K562 erythromyeloblastoid cell culture, we demonstrated changes in gene expression of Alu repeats, members of evolutionarily young AluY subfamilies (human mobile SINE elements), and in the DNA methylation level of AluYb8 during camptothecin (CAM)-induced apoptosis. The AluY-RNA level increased about 10 times 24 h and 20 times 48 h after exposure to CAM vs. proliferating cells. Using methylation-specific (MSP) PCR and high-resolution melting (HRM), we showed that the overall AluYb8-DNA methylation level remained intact throughout the apoptotic stages. Using DNA sequencing after bisulfite conversion, we established that at the CpG site, located in the A'-box of the AluYb8 gene promoter, the methylation level decreased significantly during different apoptotic stages. Apparently, it is reduced CpG methylation at the A'-box of the AluYb8 gene promoter, discovered in this work, that is one of the possible factors which account for increased expression of AluY repeats during K562 cell apoptosis. We assume that increased gene expression of evolutionarily young AluY repeats plays an important role in the implementation of the cellular apoptotic pathway.     

H-Ferritin-Regulated MicroRNAs Modulate Gene Expression in K562 Cells

In a previous study, we showed that the silencing of the heavy subunit (FHC) offerritin, the central iron storage molecule in the cell, is accompanied by a modification in global gene expression. In this work, we explored whether different FHC amounts might modulate miRNA expression levels in K562 cells and studied the impact of miRNAs in gene expression profile modifications. To this aim, we performed a miRNA-mRNA integrative analysis in K562 silenced for FHC (K562^shFHC) comparing it with K562 transduced with scrambled RNA (K562^shRNA). Four miRNAs, namely hsa-let-7g, hsa-let-7f, hsa-let-7i and hsa-miR-125b, were significantly up-regulated in silenced cells. The remarkable down-regulation of these miRNAs, following FHC expression rescue, supports a specific relation between FHC silencing and miRNA-modulation. The integration of target predictions with miRNA and gene expression profiles led to the identification of a regulatory network which includes the miRNAs up-regulated by FHC silencing, as well as91 down-regulated putative target genes. These genes were further classified in 9 networks; the highest scoring network, “Cell Death and Survival, Hematological System Development and Function, Hematopoiesis”, is composed by 18 focus molecules including RAF1 and ERK1/2. We confirmed that, following FHC silencing, ERK1/2 phosphorylation is severely impaired and that RAF1 mRNA is significantly down-regulated. Taken all together, our data indicate that, in our experimental model, FHC silencing may affect RAF1/pERK1/2 levels through the modulation of a specific set of miRNAs and add new insights in to the relationship among iron homeostasis and miRNAs.     

HERG1 Currents in Native K562 Leukemic Cells

The human ether-a-go-go related gene (HERG1) K⁺ channel is expressed in neoplastic cells, in which it was proposed to play a role in proliferation, differentiation and/or apoptosis. K562 cells (a chronic myeloid leukemic human cell line) express both the full-length (herg1a) and the N-terminally truncated (herg1b) isoforms of the gene, and this was confirmed with Western blots and coimmunoprecipitation experiments. Whole-cell currents were studied with a tail protocol. Seventy-eight percent of cells showed a HERG1-like current: repolarization to voltages negative to −40 mV produced a transient peak inward tail current, characteristic of HERG1 channels. Cells were exposed to a HERG-specific channel blocker, E4031. Half-maximal inhibitory concentration (IC₅₀) of the blocker was 4.69 nm. The kinetics of the HERG1 current in K562 cells resembled the rapid component of the native cardiac delayed rectifier current, known to be conducted by heterotetrameric HERG1 channels. Fast and slow deactivation time constants at −120 mV were 27.5 and 239.5 ms, respectively. Our results in K562 cells suggest the assembling of heterotetrameric channels, with some parameters being dominated by one of the isoforms and other parameters being intermediate. Hydrogen peroxide was shown to increase HERG1a K⁺ current in heterologous expression systems, which constitutes an apoptotic signal. However, we found that K562 HERG1 whole-cell currents were not activated by H₂O₂.     

Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70

ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in other proteins.     

应用基因芯片筛选伊马替尼和尼洛替尼处理K562 细胞表达差异基因

目的:探讨两种酪氨酸激酶抑制剂(TKIs)处理K562细胞的基因表达谱变化,为认识慢性粒细胞白血病(CML)的发病机制、耐药机制提供新的思路,同时也为治疗寻找潜在重要靶标分子。方法:利用GEO数据库下载慢性粒细胞细胞系(K562)基因表达芯片数据,通过差异基因的筛选,趋势分析、GO分析,信号通路分析,最后获得的重要差异表达核心基因,并建立相互作用网络。结果:获得显著表达差异基因1000,通过趋势分析、功能富集分析及信号通路分析提示主要涉及到代谢途径、细胞凋亡、癌症的途径、细胞周期、p53信号通路。相互作用网络分析及同表达相互作用网络分析,得到重要的核心节点基因:AK2、ADSL、PKLR、PKM、SHMT2、ATIC、LDHA、ENO1、CTH、GOT1;YARS、CYP3A5、CTH、GYPA、ALAS2、MTHFD2、BLVRB、GUK1、CTSH、LMO2。结论:利用生物信息学的方法,分析慢性粒细胞白血病细胞基因芯片得到参与不同TKIs处理K562细胞的重要的细胞功能及信号通路主要涉及代谢通路及增殖凋亡信号途径,并且寻找到核心节点基因,为认识K562的耐药机制及治疗靶点提供新的思路。     

Megakaryocytic Differentiation of K562 Cells Induced by PMA Reduced the Activity of Respiratory Chain Complex IV

Mitochondria are involved in the regulation of cell differentiation processes, but its function changes and molecular mechanisms are not yet clear. In this study, we found that mitochondrial functions changed obviously when K562 cells were induced to megakaryocytic differentiation by phorbol 12-myristate 13-acetate (PMA). During the cell differentiation, the reactive oxygen species (ROS) level was increased, mitochondrial membrane potential declined and respiratory chain complex IV activity was decreased. Treatment with specific inhibitor of mitochondrial respiratory chain complex IV led to a significant inhibition in mitochondrial membrane potential and reduction of PMA-induced cell differentiation. However, treatment with cyclosporine A, a stabilization reagent of mitochondrial membrane potential, did not improve the down-regulation of mitochondrial respiratory chain complex IV induced by PMA. Furthermore, we found that the level of the complex IV core subunit COX3 and mitochondrial transport-related proteins Tim9 and Tim10 were decreased during the differentiation of K562 cells induced by PMA, suggesting an important role of these factors in mitochondrial functional changes. Our results suggest that changes in mitochondrial functions are involved in the PMA-induced K562 cell differentiation process, and the maintenance of the steady-state of mitochondrial functions plays a critical role in the regulation of cell differentiation.     

ZnPcH1介导的光动力疗法对K562细胞的作用及其机制研究

探讨新型光敏剂ZnPcH1介导的光动力疗法对K562细胞的杀伤效应及其杀伤机制.应用MTT比色法检测光动力疗法对K562细胞增殖能力的影响;采用AO/EB荧光染色法、DNA片段化分析、TUNNEL、AnnexinV-FTTC/PI双染法等检测ZnPcH1-PDT诱导K562细胞的死亡方式;以RT-PCR法检测ZnPcH...     

Large Terminase Conformational Change Induced by Connector Binding in Bacteriophage T7

During bacteriophage morphogenesis DNA is translocated into a preformed prohead by the complex formed by the portal protein, or connector, plus the terminase, which are located at an especial prohead vertex. The terminase is a powerful motor that converts ATP hydrolysis into mechanical movement of the DNA. Here, we have determined the structure of the T7 large terminase by electron microscopy. The five terminase subunits assemble in a toroid that encloses a channel wide enough to accommodate dsDNA. The structure of the complete connector-terminase complex is also reported, revealing the coupling between the terminase and the connector forming a continuous channel. The structure of the terminase assembled into the complex showed a different conformation when compared with the isolated terminase pentamer. To understand in molecular terms the terminase morphological change, we generated the terminase atomic model based on the crystallographic structure of its phage T4 counterpart. The docking of the threaded model in both terminase conformations showed that the transition between the two states can be achieved by rigid body subunit rotation in the pentameric assembly. The existence of two terminase conformations and its possible relation to the sequential DNA translocation may shed light into the molecular bases of the packaging mechanism of bacteriophage T7.     

Changes in the Level of DNA Damage in Mouse Cells Induced by Atmospheric Factors

Biophysics - Abstract—Changes in the level of DNA damage induced by atmospheric factors were evaluated from the percentage of tail DNA (%TDNA) in the comet assay of mouse cells for blood...     

Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain

Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs). We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.     

Ideas in Theoretical Biology Origin of Cancerous Cells from Tumours

With a previous paper (Niu & Wang, 1995), a general, hypothetical outline of the mechanism of carcinogenesis was proposed. With reference to the fact of starvation-induced hypermutation in micro-organisms, we propose that the hypoxia commonly seen in the cells at the centre of solid tumours might also result in hypermutation, and then p53-dependent programmed cell death. Like the apparently adaptive mutations in micro-organisms, only those genes (e.g. p53) that enable the cells to escape from apoptosis may be selected.     

Heme-Oxygenases during Erythropoiesis in K562 and Human Bone Marrow Cells

In mammalian cells, heme can be degraded by heme-oxygenases (HO). Heme-oxygenase 1 (HO-1) is known to be the heme inducible isoform, whereas heme-oxygenase 2 (HO-2) is the constitutive enzyme. Here we investigated the presence of HO during erythroid differentiation in human bone marrow erythroid precursors and K562 cells. HO-1 mRNA and protein expression levels were below limits of detection in K562 cells. Moreover, heme was unable to induce HO-1, at the protein and mRNA profiles. Surprisingly, HO-2 expression was inhibited upon incubation with heme. To evaluate the physiological relevance of these findings, we analyzed HO expression during normal erythropoiesis in human bone marrow. Erythroid precursors were characterized by lack of significant expression of HO-1 and by progressive reduction of HO-2 during differentiation. FLVCR expression, a recently described heme exporter found in erythroid precursors, was also analyzed. Interestingly, the disruption in the HO detoxification system was accompanied by a transient induction of FLVCR. It will be interesting to verify if the inhibition of HO expression, that we found, is preventing a futile cycle of concomitant heme synthesis and catabolism. We believe that a significant feature of erythropoiesis could be the replacement of heme breakdown by heme exportation, as a mechanism to prevent heme toxicity.     

Genomic Background and Generation Time Influence Deleterious Mutation Rates in Daphnia

Understanding how genetic variation is generated and how selection shapes mutation rates over evolutionary time requires knowledge of the factors influencing mutation and its effects on quantitative traits. We explore the impact of two factors, genomic background and generation time, on deleterious mutation in Daphnia pulicaria, a cyclically parthenogenic aquatic microcrustacean, using parallel mutation-accumulation experiments. The deleterious mutational properties of life-history characters for individuals from two different populations, and for individuals maintained at two different generation times, were quantified and compared. Mutational properties varied between populations, especially for clutch size, suggesting that genomic background influences mutational properties for some characters. Generation time was found to have a greater effect on mutational properties, with higher per-generation deleterious mutation rates in lines with longer generation times. These results suggest that differences in genetic architecture among populations and species may be explained in part by demographic features that significantly influence generation time and therefore the rate of mutation.