product interaction. Gln113Ala mutation results in about 25 % decrease in SAMe production compared to the wild type, while SAMe formation of Pro115Gly is normal. Although Gln113 directly interacts with the oxygen atom of Met or SAMe via its side chain nitrogen atom, mutation of this residue does not completely prevent Met to bind at the active site. In addition, the Gln113Ala and the Ser114Ala mutant structures show asymmetrical active sites; one is empty, while the other is bound with substrates/products. In contrast to Pro115Gly mutant, its structure shows symmetrical active sites which both are fully occupied by substrates or products as found in the wild-type structure.
adsorption with chromatin removed 85-100% of reactivity to (H2A-H2B)-DNA, (H3-H4)2- DNA, and native DNA. Individual sera often bound to several different epitopes on
chromatin, with some epitopes requiring quaternary protein-DNA interactions. These results are consistent with chromatin being a potent immunogenic stimulus in SLE. Taken together with previous studies, we suggest that antibody activity to the (H2A-H2B)-DNA component signals the […]
The INM in most cell types interacts with condensed and/or silenced chromatin. By contrast, studies in yeast and metazoan cells have established functional links between specific Nups and transcriptionally active genes. Thus, the interfaces between NPCs and the INM are likely transitional zones between chro- matin states. We have uncovered functional interactions between Nup170p and chromatin domains that generally reside adjacent to the NE, including subtelomeric and telomeric regions. We propose that Nup170p establishes a platform at the NPC that interacts with these chromatin regions and promotes transcriptional repression of RP genes and subtelo- meric chromatin. In the context of subtelomeric chromatin, Nup170p functionally interacts with RSC and Sir4p, facilitating Sir4p assembly on subtelomeric heterochromatin, chromatin association with the NE, and repression of resident gene expression.
In addition, like in animals, plant H1 variants interplay with the DNA methylation machinery, particularly af- fecting TEs. H1 also affects DNA methylation at the genic regions, although only a few have been experimen- tally interrogated so far [22, 31–33]. Despite their ex- pected fundamental role in chromatin accessibility, very little was known about the specific impact of H1 at the structural, epigenetic, and gene expression level in plants. In this study, we unveiled distinct effects of H1 function on nucleosome occupancy and transcriptional activity over heterochromatin and protein-coding genes, respectively (model presented in Fig. 5). We further un- veiled that H1 is strictly required for heterochromatin formation but not for the establishment of heterochro- matic hallmarks, that H1 provides spatial regularity in nanodomain chromatin compaction and distribution which coincides with a role in the maintenance of H3K27me3 in euchromatin, and that in fine H1-medi- ated chromatin organization secures a proper control of specific developmental transitions.
While changing the binding pocket may increase hydrogen bond formation, this also alters the conformation of the inhibitor.
Three multi-drug resistant HIV-1 protease clinical isolates were selected from patients attending the Wayne State University infectious diseases clinic and failing antiviral treatment therapy on PI based regimens. To explore the structural mechanisms resulting in treatment failure, we performed 40ns MD simulations on the Detroit MDR series. Our results indicate a novel structural role for the I47V, V32I, I54M and L90M resistance mutations.
bond is 1.8 Å, and those bonds in the intermediate II were in great agreement with that (Fig. 3.4D). The cyclic intermediate II was stabilized by extensive hydrogen bonds from both the backbone and the side-chains as well as hydrophobic interactions (Fig.
3.4E). Tyr102 and Arg105 specifically recognized succinyl group. The catalytic residue H158 formed a hydrogen bond with 2’-OH of N-ribose, and deprotonated it to promote the nucleophilic attack of succinyl carbon by 3’-OH. Residue Gln140 was absolutely conserved in all mammalian sirtuins, formed a hydrogen bond with N- ribose via the backbone oxygen, and played a key role in positioning the N-ribose during the reaction. The highly conserved residues, Val221, interacted with and stabilized the lysine side chain via a hydrogen bond of its backbone oxygen with ε-N of lysine. The benzyl ring of Phe70 paralleled with N-ribose ring and formed π-π hydrophobic interactions, thus stabilizing the intermediate at the active site. All those interactions stabilized and positioned the cyclic intermediate at the active site in a conformation that is favorable for the turn-over.
inclusive of their branching angles obtained from previ- ous morphometric studies with human airways [68, 85].
A stack-based algorithm traverses the airway tree and determines the highest branch to designate for closure to reproduce the ventilation defect in precise anatomic locations of the model that correspond to the anatomic locations of the image. Each branch within the airway tree is modeled assuming laminar flow in a compliant walled tube and hence requires a distinct flow resistance and inertance partitioned via a shunt airway wall compli- ance with each parameter for an airway branch a func- tion of its length, diameter and wall material properties (Eq. 13). The terminal airways are then connected to a gas compression associated with the alveolar gas in par- allel with a constant-phase tissue model all scaled to the appropriate volume. Impedance of the entire tree as well as ventilation distribution to all alveolar regions can be calculated by the appropriate series and parallel calcula- tions also through a stack-based algorithm. All airway diameters are scaled to FRC, and the subsequent lung volume at FRC is distributed evenly among the terminal alveolar units.
Abstract: Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.
venom enzymes like batroxobin and reptilase (15). Thus, there is controversy surrounding the role of “B:b” interactions in fibrin polymerization.
1.4 Recombinant Fibrinogen
Because plasma fibrinogen binds proteins like factor XIII, fibronectin and plasminogen, plasma-derived fibrinogen often co-purify with these proteins even with extensive purification procedures. The natural heterogeneity of plasma fibrinogen due to variations in mRNA processing, posttranslational modification and proteolysis in the circulation also makes plasma preparation not ideal for well-controlled experiments. The use of homogeneous, recombinant fibrinogen circumvents most of these problems and also permits synthesis of variant fibrinogens. This system is a powerful tool in identifying residues critical to normal fibrin polymerization. Recombinant fibrinogens can also be used to study and understand the details involved in dysfibrinogenemia cases which are abnormalities associated with genetic variants. The vast majority of dysfibrinogenemia patients are heterozygous to the mutation which means both the normal and abnormal copies are present in their plasma. The recombinant system allows homogeneous mutated fibrinogen to be synthesized and used to determine the molecular basis for the functional impairment. It is important to note that plasma and recombinant fibrinogen molecules are essentially the same as shown by multiple experiments (16).
Physiological neuronal activity induces DNA double-strand breaks
Recently, several groups have described a perplexing phenomenon that occurs in response to neuronal activity: the formation of DNA double-strand breaks (DSBs; Figure 1B).
Physiologically relevant neuronal activity, such as that elicited by exploration of a novel environment, induced DSB formation in neurons of memory-relevant brain regions such as the hippocampus . Madabhushi et al.  recently provided a mechanism for these activity-induced DSBs by demonstrating a role for the type II topoisomerase Topo IIβ in break formation. Moreover, through genome-wide profiling of the DSB-associated phosphorylated histone variant γH2AX, they identified just twenty-one genomic loci that accrue DSBs in response to NMDA-mediated neuronal activity. Remarkably, a majority of the sites exhibiting γH2AX enrichment encompassed the bodies of IEGs, were flanked by CTCF binding sites, and break induction was shown to be necessary and sufficient for transcriptional activation of c-fos and Npas4. Furthermore, inhibition of the non-
 . In this study, they observed that nucleosomes impose a bar- rier for RNAPII progression, increasing pause density and duration
and decreasing RNAPII apparent velocity. According to their model, when RNAPII finds a nucleosome on its way along DNA, it tends to pause and backtrack. RNAPII lacks the ability to unwrap nucleo- somes, so it has to happen either spontaneously or via the action of chromatin remodelers. But what happens with the histones and how do nucleosomes re-assemble when RNAPII transcribes a region? It has been proposed that DNA forms a loop that allows DNA behind RNAPII to interact with the histones of partially unwrapped nucleosomes. This would permit an in cis histone transfer to DNA, upstream the original position of the nucleosome, and guarantee the correct re-establishment of nucleosome posi- tioning after transcription. Other in vitro studies performed by Michelle D. Wang’s group, suggest that the positive torque exerted by RNA polymerase on DNA can contribute to destabilize H2A-H2B dimers from nucleosomes, and thus favor their disassembly in the way of RNAPII  . In any case, nucleosome disassembly and reassembly in vivo are probably facilitated by the action of chro- matin remodelers and histone chaperones  . In a more recent publication, Bustamante’s group used their in vitro transcription system to study in detail the influence of different histone tail modifications and direct histone-DNA interactions on transcription
tissue damage and cell death, nuclear chromatin is cleaved into nucleosomes, which are released extracellularly 232 and further degraded into individual histones. Recent studies demonstrate their direct toxicity to endothelial cells as well as causing activation of platelets 275 and leukocytes to promote thrombosis 276 , disturb the microvascular circulation and stimulate cytokine release 271 . In animal models, elevation of circulating histones is observed in inflammatory diseases such as sepsis 213 , acute kidney injury 277 , liver injury 278 and peritonitis 279 . Histone infusion causes animal death through MODS, which can be rescued by anti-histone antibodies 271 . The major mechanism for toxicity is due to histones binding phospholipids on cell membranes resulting in calcium influx and cellular injury 271 . In clinical practice, high circulating histone levels have been found in patients with severe blunt trauma and sepsis 271 . These levels are significantly associated with injury severity scores and sequential organ failure assessment (SOFA) scores as well as the incidence of respiratory and circulatory failure 271 . It is known that extensive cell death occurs in severe, particularly necrotising pancreatitis. However, there has been no direct evidence of linking circulating histones with the severity of acute pancreatitis.
The ability of VCP to bind heparan sulfate proteoglycan molecules adds a new dimension to its role in modulating the host immune response. In previous studies, the ability of VCP to bind heparin was found to permit uptake by mast cells – possibly allowing for tissue persistence over an extended time. In addition, earlier studies have shown that binding to heparin-like molecules on the surface of endothelial cells can block chemokine adherence, resulting in reduced chemotactic signaling. The next step was to determine if VCP, bound to the endothelial cell surface, could interfere with antibody binding. In this study, flow cytometry was used to demonstrate that VCP is able to bind the surface of endothelial cells, interfering with antibody binding. More importantly, this study demonstrates that addition of VCP significantly decreases the amount of antibody able to attach to HUVECs in a dose-dependent manner. It is postulated that VCP, binding to heparin-like molecules on the surface of endothelial cells, prevents antibody adherence. This binding may therefore block antibody attachment through steric
Alain Verreault, University of Montreal and speaker at the EuroDYNA session at ELSO, focuses his research on how chemicals in the environment affect DNA. Verreault’s research has many implications for the treatment of cancer using chemotherapy. He has found that a process called acetylation, when an acetyl group is added to a protein, globally affects the proteins that package DNA (known as histones) during DNA replication. Both the acetylation of histones and its timely removal are important for efficient DNA repair and cell survival in response to DNA damage. For instance, when the genes HST3 and HST4 were removed from yeast cells, acetylation could no longer be removed from histone proteins, which resulted in increased DNA damage, both spontaneous and in response to chemotherapeutic agents that damage DNA. This research could prove tremendously important to cancer treatment, but Verreault also emphasised “I suspect that other acetylation sites play a role in higher eukaryotes and more research is needed”.
responsive Mef2 target genes) and account for 17% of all short-term GH-responsive class I male-specific genes (Table S10D in Wauthier et al. 2010). The functional significance of the rapid activation of Mef2 target genes by GH in male liver is unknown. Two of the four vertebrate Mef2 genes, Mef2a and Mef2d, are expressed at significant levels in mouse liver and the other two forms are expressed at low levels, as judged by their microarray signal intensities. The Mef2 genes themselves did not respond to GH treatment, suggesting that GH may regulate Mef2 activity post-translationally, e.g., by phosphorylation. Other studies have reported that Mef2a, Mef2c and Mef2d RNA and protein are present in hepatic stellate cells, which comprise 5-8% of resident liver cells and are activated in a Mef2-dependent manner to a myofibroblast-like phenotype under pathological conditions leading to liver fibrosis and cirrhosis (Sato et al. 2003; Wang et al. 2004). The association of Mef2-regulated genes with myofibroblast/smooth muscle function is consistent with the preferential expression of Mef2 protein in this liver cell type and with the activation of these Mef2 genes under conditions of hepatic stellate cell activation (Wang et al. 2004). Furthermore, hepatic stellate cells are strongly activated in hepatocellular carcinoma, where Mef2 protein is highly expressed (Bai et al. 2008), suggesting that Mef2 plays a key role in hepatocellular carcinoma pathogenesis. In this context our observation that male liver is more responsive to rapid GH induction of Mef2 target gene expression is intriguing, insofar as it suggests that GH activation of Mef2 signaling could be an important factor in the widespread greater susceptibility of males to liver cancer (De Maria et al. 2002). Although STAT5 is a known mediator of GH-
Several strategies have been devised for the quantitative assessment of total genomic deoxycytosine (dC) and deoxymethylcytosine content, as well as the methylation status of specific sequences. These are the subject of a recent review (5). At present, the most precise and generally applicable techniques for sequence-specific methylation analysis rely on bisulfite modification of DNA. Treating DNA with bisulfite deaminates cytosine bases to form uracil, but does not affect methylcytosine. Thus, PCR amplification and sequencing of bisulfite treated DNA allows precise quantitation of the methylation status of any desired CG pair (6). This approach, coupled with regional methylation of dC bases in promoter reporter constructs and DNaseI hypersensitivity analysis of chromatinstructure in the region, provides information regarding both the presence and functional significance of the methylation patterns. Further confirmation may be obtained by demethylating DNA with the irreversible DNA methyltransferase inhibitor 5-azacytidine (5-azaC), then comparing effects on gene expression and methylation patterns. In this report we describe the methods utilized to compare the methylation patterns of the ITGAL (CD11a) promoter in T cells and fibroblasts, and of the PRF1 (perforin) promoters in T cells, an NK cell line and in fibroblasts, and how cassette or “patch” methylation may be used to test the effects of regional methylation on ITGAL and PRF1 promoter function. We also describe the use of DNaseI hypersensitivity assays to probe the chromatinstructure around the same genes in representative cells with differential CD11a and perforin expression, and the use of DNA methyltransferase inhibition to confirm transcriptionally relevant changes in DNA methylation patterns.
ABSTRACT The members of the Sir2 family, or Sirtuins, have garnered considerable attention because of their key roles as metabolic sensors and mediators of cell survival under stress. Sirtuins may play roles in myriad human pathologies such as cancer, neurological diseases, malaria, leishmaniasis and hormone-related disorders. They are present from prokaryotes to humans and show a high degree of functional diversification that has led to two different enzymatic activities, a wide range of substrates and a highly diversified pattern of cellular localization. Throughout chromatin evolution, Sirtuins have maintained an intimate functional relationship in regulating its structure and function via their targeting of histones, particularly H4K16Ac, as well as other non- histone chromatin proteins. This link permitted fast communication from metabolic fluctuations to chromatin allowing efficient adaptation to environmental stimuli. Therefore, understanding the common path of Sirtuins and chromatin development over the course of evolution might be important for understanding not only the remarkable diversity of functions of these proteins in mammals, but also the path followed by chromatin evolution. Herein is provided an overview of current knowledge of Sirtuin function, from bacteria to humans, including a discussion on its implications for chromatin dynamics, organization and integrity.
1.5.6 C-type natriuretic peptide
CNP is the most highly conserved natriuretic peptide across species, including humans, rodents, reptiles and fish (Del Ry et al., 2006b). In addition, studies of the lineage of natriuretic peptide genes have suggested that ANP and BNP originated from CNP via gene duplication (Inoue et al., 2003). The human CNP gene (Nppc) is located on chromosome 2 and contains two exons and one intron (Ogawa et al., 1992). CNP is synthesised as pre- proCNP comprising 126 amino acids. The pre-proCNP is then cleaved into pro-CNP (103 amino acids) via the removal of signal peptide by signal peptidase. Pro-CNP is the form in which the peptide is stored. Subsequently, furin, a protein convertase that residents in the trans-Golgi network, cleaves pro-CNP to yield CNP-53. CNP-53 is then converted to biological active CNP-22 by an unidentified mechanism (Del Ry et al., 2006b) (Figure 6). Targeted disruption of CNP in mice causes severe dwarfism due to impairment of endochondral ossification, and high mortality before adulthood (Komatsu et al., 2002). Similar phenotypes are observed in humans with conditions involving inactivating mutations in CNP (Hisado-Oliva et al., 2018). Furthermore, several genome-wide association studies (GWAS) have established a relationship between Nppc and height (Estrada et al., 2009, Wood et al., 2014). This indicates that CNP is crucial for bone development and growth. Interestingly, the highest CNP expression in adult mice is found in the uterus and ovary (Stepan et al., 2000), and a function of CNP in reproduction has been demonstrated (Gutkowska et al., 1999). Other sites with significant expression of CNP mRNA include the CVS, skin, lungs, tongue, liver, kidney and stomach (Stepan et al., 2000). This wide distribution of CNP expression implies a multifunctional role for this peptide.