SEARCH · bioRxiv Science

Results for “Biochemistry”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,513 records · Page 84Linked to original sources

bioRxiv2019

Basis for discrimination by engineered CRISPR/Cas9 enzymes

CRISPR/Cas9 is a programmable genome editing tool that has been widely used for biological applications. While engineered Cas9s have been reported to increase discrimination against off-target cleavage compared with wild type Streptococcus pyogenes (SpCas9) in vivo, the mechanism for enhanced specificity has not been extensively characterized. To understand the basis for improved discrimination against off-target DNA containing important mismatches at the distal end of the guide RNA, we performed kinetic analyses on the high-fidelity (Cas9-HF1) and hyper-accurate (HypaCas9) engineered Cas9 variants. While DNA unwinding is the rate-limiting step for on-target cleavage by SpCas9, we show that chemistry is seriously impaired by more than 100-fold for the high-fidelity variants. The high-fidelity variants improve discrimination by slowing the rate of chemistry without increasing the rate of DNA rewinding--the kinetic partitioning favors release rather than cleavage of a bound off-target substrate because chemistry is slow. Further improvement in discrimination may require engineering increased rates of dissociation of off-target DNA.

biochemistry↗

bioRxiv2019

Mutational mimics of allosteric effectors: a genome editing design to validate allosteric drug targets

Development of drugs that allosterically regulate enzyme functions to treat disease is a costly venture. Screening mutations that mimic allosteric effectors in vitro will identify therapeutic regulatory targets enhancing the likelihood of developing a disease treatment at a reasonable cost. We demonstrate the potential of this approach utilizing human liver pyruvate kinase (hLPYK) as a model. Inhibition of hLPYK was the first desired outcome of our screen. We identified individual point mutations that: 1) mimicked allosteric inhibition by alanine, 2) mimicked inhibition by protein phosphorylation, and 3) prevented binding of fructose-1,6-bisphosphate (Fru-1,6-BP). Our second desired screening outcome was activation of hLPYK. We identified individual point mutations that: 1) prevented hLPYK from binding alanine, the allosteric inhibitor, 2) prevented inhibitory protein phosphorylation, or 3) mimicked allosteric activation by Fru-1,6-BP. Combining the three activating point mutations produced a constitutively activated enzyme that was unresponsive to regulators. Expression of a mutant hLPYK transgene containing these three mutations in a mouse model was not lethal. Thus, mutational mimics of allosteric effectors will be useful to confirm whether allosteric activation of hLPYK will control glycolytic flux in the diabetic liver to reduce hepatic glucose production and, in turn, reduce or prevent hyperglycemia.

biochemistry↗

bioRxiv2019

DEAD-box protein family member DDX28 is a negative regulator of HIF-2α and eIF4E2-directed hypoxic translation

Hypoxia occurs when there is a deficiency in oxygen delivery to tissues and is connected to physiological and pathophysiological processes such as embryonic development, wound healing, heart disease and cancer. The master regulators of oxygen homeostasis in mammalian cells are the heterodimeric hypoxia-inducible transcription factors HIF-1 and HIF-2. The oxygen-labile HIF-2 subunit has not only been implicated in transcription, but also as a regulator of eIF4E2-directed hypoxic translation. Here, we have identified the DEAD-box protein family member DDX28 as a novel interactor and negative regulator of HIF-2 that suppresses its ability to activate eIF4E2-directed translation. We demonstrate that stable silencing of DDX28 via shRNA in hypoxic human U87MG glioblastoma cells caused an increase, relative to control, to: HIF-2 protein levels, the ability of eIF4E2 to bind the m7GTP cap structure, and the translation of select eIF4E2 target mRNAs. DDX28 depletion elevated both nuclear and cytoplasmic HIF-2, but HIF-2 transcriptional activity did not increase possibly due to its already high nuclear abundance in hypoxic control cells. Depletion of DDX28 conferred a proliferative advantage to hypoxic, but not normoxic cells, which is likely a consequence of the translational upregulation of a subset of hypoxia-response mRNAs. DDX28 protein levels are reduced in several cancers, including glioma, relative to normal tissue. Therefore, we uncover a regulatory mechanism for this potential tumor suppressor in the repression of HIF-2- and eIF4E2-mediated translation activation of oncogenic mRNAs.

biochemistry↗

bioRxiv2019

Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites

For protein mutagenesis, a common expectation is that important positions will behave like on/off \"toggle\" switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: \"rheostat\" positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostat effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of \"local\" positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostat outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.

biochemistry↗

bioRxiv2019

Acylcarnitine Metabolomic Profiles Inform Clinically-Defined Major Depressive Phenotypes

BackgroundAcylcarnitines have important functions in mitochondrial energetics and {beta}-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profiles can help biochemically distinguish the three phenotypic subtypes of major depressive disorder (MDD)--(core depression (CD+), anxious depression (ANX+), and neurovegetative symptoms of melancholia (NVSM+))--following treatment with a selective serotonin reuptake inhibitor (SSRI).\n\nMethodsDepressed outpatients (n=240) from the Mayo Clinic Pharmacogenomics Research Network were treated with citalopram or escitalopram for eight weeks. Plasma samples collected at baseline and eight weeks post-treatment were profiled for multiple-, short-, medium- and long-chain acylcarnitine levels using AbsoluteIDQ(R)p180-Kit and LC-MS. Linear mixed effects models were used to examine whether acylcarnitine levels discriminate the clinical phenotypes at baseline or eight weeks post-treatment, and whether temporal changes in acylcarnitine profiles differ between groups.\n\nResultsAt baseline, significantly lower concentrations of short- and long-chain acylcarnitines were found in CD+ and NVSM+ compared to ANX+, and the short-chain acylcarnitines remained lower after eight weeks. At eight weeks, the medium- and long-chain acylcarnitines were significantly lower in NVSM+ compared to ANX+. Regarding changes baseline to week eight, short-chain acylcarnitine levels significantly increased in CD+ and ANX+, and medium- and long-chain acylcarnitines significantly decreased in NVSM+ and CD+.\n\nConclusionsIn depressed patients treated with SSRIs, {beta}-oxidation and mitochondrial energetics as evaluated by levels and changes in acylcarnitines may provide the biochemical basis of the clinical heterogeneity of MDD, especially when combined with clinical characteristics.

biochemistry↗

bioRxiv2019

Do neutral protein positions really exist? A case study with allostery in human liver pyruvate kinase

Understanding how each residue position contributes to protein function has been a long-standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate kinase (hLPYK), including altered allosteric coupling. To facilitate a comparison of which characteristics determine when a nonconserved position does vs. does not contribute to function, the goal of the current work was to identify neutral positions in hLPYK. However, existing hLPYK data showed that three features commonly associated with neutral positions - high sequence entropy, high surface exposure, and alanine scanning - lacked the sensitivity needed to guide experimental studies. We used multiple evolutionary patterns identified in a sequence alignment of the PYK family to identify which positions were least patterned, reasoning that these were most likely to be neutral. Nine positions were tested with a total of 117 amino acid substitutions. Although exploring all potential functions is not feasible for any protein, five parameters associated with substrate/effector affinities and allosteric coupling were measured for hLPYK variants. For each position, the aggregate functional outcomes of all variants were used to quantify a "neutrality" score. Three positions showed perfect neutral scores for all five parameters. Furthermore, the nine positions showed larger neutral scores than 17 positions located near allosteric binding sites. Thus, our strategy successfully enriched the dataset for positions with neutral and modest substitutions.

biochemistry↗

bioRxiv2019

Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation

Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as it commits to and develops through gametocytogenesis. The gametocyte-associated transcriptome is significantly different from that of the asexual parasites, with dynamic gene expression shifts characterizing early, intermediate and late-stage gametocyte development and results in differential timing for sex-specific transcripts. The striking transcriptional dynamics suggest strict transcriptional control during gametocytogenesis in P. falciparum, which we propose is mediated by putative regulators including epigenetic mechanisms (driving active repression of proliferation-associated processes) and a cascade-like expression of ApiAP2 transcription factors. The gametocyte transcriptome serves as the blueprint for sexual differentiation and will be a rich resource for future functional studies on this critical stage of Plasmodium development, as the intraerythrocytic transcriptome has been for our understanding of the asexual cycle.

biochemistry↗

bioRxiv2019

Phosphatidylinositol Cycle Disruption is Central to Atypical Hemolytic-Uremic Syndrome Caused by Diacylglycerol Kinase Epsilon Deficiency

BackgroundLoss-of-function mutations in diacylglycerol kinase epsilon (DGKE) cause a rare form of atypical hemolytic-uremic syndrome (aHUS) for which there is no treatment besides kidney transplantation. Highly expressed in kidney endothelial cells, DGKE is a lipid kinase that phosphorylates diacylglycerol (DAG) to phosphatic acid (PA). Specifically, DGKEs preferred substrate is 38:4-DAG, that is DAG containing stearic acid (18:0) and arachidonic acid (20:4). DAG is produced when phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) is cleaved by phospholipase C (PLC). A better understanding of how DGKE deficiency impacts the endothelial lipid landscape is critical to developing a treatment for this condition.\n\nMethodsWe used orthogonal methods to compare the lipid levels in two novel models of DGKE deficiency to their respective controls: an immortalized human umbilical vein endothelial cell (iHUVEC) engineered with CRISPR/Cas9 and a blood outgrowth endothelial cell (BOEC) from an affected patient. Methods included mass spectrometry lipidomics, radiolabeling of phosphoinositides with [3H]myo-inositol, and live-tracking of a transfected fluorescent PtdIns(4,5)P2 biosensor.\n\nResultsUnexpectedly, mass spectrometry lipidomics data revealed that high 38:4-DAG was not observed in the two DGKE-deficient models. Instead, a reduction in 38:4-PtdIns(4,5)P2 was the major abnormality.These results were confirmed with the other two methods in DGKE-deficient iHUVEC.\n\nConclusionReduced 38:4-PtdIns(4,5)P2--but not increased 38:4-DAG--is likely to be key to the pro-thrombotic phenotype exhibited by patients with DGKE aHUS.\n\nTRANSLATIONAL STATEMENTMutations in DGKE cause a severe renal thrombotic microangiopathy that affects young children and leads to end-stage renal disease before adulthood. DGKE preferentially phosphorylates diacylglycerol to its corresponding phosphatidic acid (PA), which is then used to synthesize PtdIns(4,5)P2 via the phosphatidylinositol cycle. Understanding the disease pathophysiology is necessary to develop a treatment to prevent this outcome. This paper describes how we applied mass spectrometry lipidomics to two novel models of DGKE deficiency to investigate how this defect impacts the levels of diacylglycerol, PA and related phosphoinositides in endothelia. Unexpectedly, our data show that the critical abnormality caused by DGKE deficiency is not high diacylglycerol, but rather low PtdIns(4,5)P2. Restoring endothelial PtdIns(4,5)P2 homeostasis may be the cornerstone to treat these patients.

biochemistry↗

bioRxiv2019

OTUB1 is a key regulator of RIG-I dependent immune signalling and is targeted for proteasomal degradation by influenza A NS1

Deubiquitylases (DUBs) regulate critical signaling pathways at the intersection of host innate immunity and viral pathogenesis. Although RIG-I activation is heavily dependent on ubiquitylation, DUBs that regulate this pathway have not been identified. Using a ubiquitin C-terminal electrophile, we profiled DUBs that function during influenza A virus (IAV) infection, and isolated OTUB1 as a key regulator of RIG-I dependent antiviral responses. OTUB1 was interferon-inducible, and interacted with RIG-I, viral PB2 and NS1. Upon infection, OTUB1 relocalised from the nucleus to mitochondrial membranes, and activated the RIG-I signaling complex via hydrolysis of K48 polyubiquitin chains and by forming a repressive complex with UBCH5c. Using a reconstituted system composed of in vitro translated [35S]IRF3, purified RIG-I, mitochondrial membranes and cytosol expressing OTUB1 variants, we recapitulated the mechanism of OTUB1-dependent RIG-I activation. A wide range of IAV NS1 proteins triggered proteasomal degradation of OTUB1, thereby antagonizing the RIG-I signaling cascade and antiviral responses.\n\nHighlightsO_LIOTUB1 is induced during influenza A virus infections in an IFN-I dependent manner\nC_LIO_LIOTUB1 regulates the RIG-I complex by hydrolysing K48-linked polyubiquitin chains and by sequestering UBCH5c to prevent K48 polyubiquitylation\nC_LIO_LIOptimal K63 versus K48 polyubiquitin chain concentrations determine RIG-I activation\nC_LIO_LIInfluenza NS1 targets OTUB1 for proteasomal degradation\nC_LI

biochemistry↗

bioRxiv2019

A cytochrome P450 from juvenile mustard leaf beetles hydroxylates geraniol, a key step in iridoid biosynthesis

Juveniles of the leaf beetle Phaedon cochleariae synthesize iridoid via the mevalonate pathway to repel predators. The normal terpenoid biosynthesis is integrated into the dedicated defensive pathway by the {omega}-hydroxylation of geraniol to 8-hydroxygeraniol. Here we identify and characterize the geraniol 8-hydroxylase as a P450 monooxygenase using integrated transcriptomic and proteomic analyses. In the fat body, 73 individual cytochrome P450s were identified. The double stranded RNA (dsRNA)-mediated knock down of CYP6BH5 led to a significant reduction of 8-hydroxygeraniol-glucoside in the hemolymph and, later, of the chrysomelidial in the defensive secretion. Heterologously expressed CYP6BH5 converted geraniol to 8-hydroxygeraniol. In addition to geraniol, CYP6BH5 also catalyzes other monoterpenols, such as nerol and citronellol, into the corresponding , {omega}-dihydroxy compounds.\n\nHighlightsO_LIThe geraniol 8-hydroxylase in Phaedon cochleariae was identified as a cytochrome P450 CYP6BH5.\nC_LIO_LIRNA interference emphasized the importance of CYP6BH5 in iridoid biosynthesis.\nC_LIO_LIIn vitro enzyme assays showed that recombinant CYP6BH5 is a substrate promiscuous enzyme, converting the {omega}-hydroxylation of geraniol, nerol, citronellol but not linalool.\nC_LIO_LIHomology modeling suggested the -OH group of the substrate plays an important role in coordinating the substrates with the enzymes catalytic cavity.\nC_LI

biochemistry↗

bioRxiv2019

TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease

Autophagy is a highly conserved catabolic process through which defective or otherwise harmful cellular components are targeted for degradation via the lysosomal route. Regulatory pathways, involving post-translational modifications such as phosphorylation, play a critical role in controlling this tightly orchestrated process. Here, we demonstrate that TBK1 regulates autophagy by phosphorylating autophagy modifiers LC3C and GABARAP-L2 on surface-exposed serine residues (LC3C S93 and S96; GABARAP-L2 S87 and S88). This phosphorylation event impedes their binding to the processing enzyme ATG4 by destabilizing the complex. Phosphorylated LC3C/GABARAP-L2 cannot be removed from liposomes by ATG4 and are thus protected from ATG4-mediated premature removal from nascent autoph-agosomes. This ensures a steady coat of lipidated LC3C/GABARAP-L2 throughout the early steps in autophagosome formation and aids in maintaining a unidirectional flow of the autophagosome to the lysosome. Taken together, we present a new regulatory mechanism of autophagy, which influences the conjugation and de-conjugation of LC3C and GABARAP-L2 to autophagosomes by TBK1-mediated phosphorylation.

biochemistry↗

bioRxiv2019

Stabilizing non-native excited states as a therapeutic strategy for targeting RNA

Many regulatory RNAs undergo changes in their structure from the dominant ground-state (GS) toward short-lived low-abundance excited-states (ES) that reorganize local elements of secondary structure. ESs are increasingly observed in vitro and implicated in the folding and biological activities of regulatory RNAs and as targets for developing therapeutics. However, whether these ESs also form with comparable abundance within the complex cellular environment remains unknown. Here, we developed an approach for assessing the relative stability and abundance of RNA ESs within the functional cellular context. The approach uses point substitution mutations to increase the population of an inactive ES relative to the active GS. The cellular activity of such ES-stabilizing mutants then provides an indirect measure of any residual population of the active GS within the functional cellular context. Compensatory rescue mutations that restore the GS are used to control for changes in cellular activity arising due to changes in sequence. The approach is applied to probe ESs in two highly conserved and functionally important regulatory RNAs from HIV-1: the transactivation response element (TAR) and the Rev response element (RRE). For both RNAs, ES-stabilizing mutations inhibited cellular activity to a degree that correlates with the extent to which they stabilize the ES relative to the GS in vitro. These results indicate that the non-native ESs of TAR and RRE likely form in cells with abundances comparable to those measured in vitro and their targeted stabilization provides a new avenue for developing anti-HIV therapeutics.

biochemistry↗

bioRxiv2019

Characterisation of the c10orf76-PI4KB complex, and its necessity for Golgi PI4P levels and enterovirus replication

The lipid kinase PI4KB, which generates phosphatidylinositol 4-phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi, and is essential for the viral replication of specific enteroviruses. We used hydrogen deuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complex-disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76-dependent enteroviruses. Intriguingly, c10orf76 was also required for proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi.\n\nHighlightsO_LIc10orf76 forms a direct complex with PI4KB, with the interface formed by a disorder-to-order transition in the kinase linker of PI4KB\nC_LIO_LIThe c10orf76 binding site of PI4KB can be phosphorylated by PKA, with phosphorylation leading to decreased affinity for c10orf76\nC_LIO_LIComplex-disrupting mutants of PI4KB and c10orf76 reveal that PI4KB recruits c10orf76 to the Golgi/TGN\nC_LIO_LIDepletion of c10orf76 leads to decreases in both active Arf1 and Golgi PI4P levels\nC_LIO_LIEnteroviruses that rely on c10orf76 for replication depend on formation of the c10orf76-PI4KB complex\nC_LI

biochemistry↗

bioRxiv2019

Girdin: an essential component of pre-replicative complex in human cells

A central event in the initiation of DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) on specific chromatin sites known as DNA replication origins. The pre-RC assembly process differs between budding and fission yeasts. In fission yeast, Sap1 directly participates in pre-RC assembly, together with the four initiation factors: ORC, Cdc18/Cdc6, Cdt1, and MCM. In metazoans, the nature of DNA replication origins is not defined and the mechanism of pre-RC assembly remains incompletely known. In this study, Girdin was identified as an essential replication initiation factor in human cells. Similar to the activity of Sap1, human Girdin binds to DNA origins, interacts with ORC, and is required for pre-RC assembly due to its essential role in recruitment of Cdc6 to DNA origins. Thus, DNA origins in human or metazoans are defined as including two elements, one bound by ORC and the other bound by Girdin.

biochemistry↗

bioRxiv2019

4-oxo-2-nonenal Adducts In HDL Are Elevated In Familial Hypercholesterolemia: Identification Of Modified Sites And Functional Consequences

The lipid aldehyde 4-oxo-2-nonenal (ONE) derived from peroxidation of n-6 polyunsaturated fatty acids and generated in parallel to 4-hydroxynonenal (HNE) is a highly reactive protein crosslinker. Crosslinking of proteins in high-density lipoprotein (HDL) by lipid peroxidation products causes HDL dysfunction and contributes to atherogenesis. While HNE is relatively well studied, the relevance of ONE in atherosclerosis and in modifying HDL has not been examined. In the present study, we found a significant increase in ONE-ketoamide (lysine) adducts in HDL derived from patients with familial hypercholesterolemia (FH) (1620 {+/-} 985.4 pmol/mg) compared to healthy controls (664 {+/-} 219.5 pmol/mg). ONE crosslinked apoA-I on HDL at a concentration of >3 mol ONE per 10 mol apoA-I (0.3 eq), which is 100-fold lower than HNE but comparable to the potent protein crosslinker, isolevuglandin. ONE-modified HDL partially inhibited the ability of HDL to protect against LPS-induced TNF and IL-1{beta} mRNA expression in murine macrophages. At 3 eq., ONE dramatically decreased the ability of apoA-I to exchange from HDL, from ~46.5% to only ~18.4% (P<0.001). Surprisingly, ONE-modification of HDL or apoA-I did not alter macrophage cholesterol efflux capacity. LC/MS/MS analysis showed modification of Lys12, Lys23, Lys96, and Lys226 of apoA-I by ONE-ketoamide adducts. Compared to other dicarbonyl scavengers, pentylpyridoxamine (PPM) was most efficacious at blocking ONE-induced protein crosslinking in HDL. Our studies show that ONE HDL adducts are elevated in FH who have severe hypercholesterolemia and atherosclerosis and causes HDL dysfunction. We demonstrate the use of PPM in preferentially scavenging ONE in biological systems.

biochemistry↗

bioRxiv2019

RNA strand invasion activity of the Polycomb complex PRC2

Epigenetic regulation is conveyed through information encoded by specific chromatin features. Non-canonical nucleic acid structures could in principle also convey biological information but their role(s) in epigenetic regulation is not known. Polycomb Group (PcG) proteins form memory of transient transcriptional repression events that is necessary for development. In Drosophila, PcG proteins are recruited to specific DNA sequences, Polycomb Response Elements (PREs). PREs are switchable memory elements that can exist in repressed, active, or unengaged states 1,2. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. Biochemically, PcG protein complexes modify chromatin to maintain gene repression 1,3,4. However, PcG proteins also interact with both RNA and DNA, and RNA is implicated in the targeting of PcG function. We find that R-loops, three-stranded nucleic acid structures formed when an RNA hybridizes to its complementary DNA and displaces the other DNA strand 5, form at many PREs in Drosophila embryos, and correlate with the repressive state. R-loops are recognized by the PcG complex PRC1 in vitro. Unexpectedly, we find that the PcG complex PRC2 has RNA strand invasion activity, which can drive formation of RNA-DNA hybrids, the key component of R-loops. Our results suggest a new mechanism for targeting PcG function through R-loop formation by PRC2 and recognition by PRC1. More generally, our findings suggest formation and recognition 6 of non-canonical nucleic acid structures as an epigenetic mechanism.

biochemistry↗

bioRxiv2019

Structural basis for ligand-induced inactivation of protein tyrosine receptor type Z (PTPRZ): Physiological relevance of head-to-toe RPTP dimerization

Protein tyrosine phosphatase receptor type Z (PTPRZ) has two receptor isoforms (PTPRZ-A and -B) containing tandem PTP-D1 and -D2 domains intracellularly, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular region of PTPRZ leads to the inactivation of PTPase, thereby inducing oligodendrocyte precursor cell (OPC) differentiation and myelination in the CNS. However, the mechanisms responsible for the ligand-induced inactivation of PTPRZ remain unclear. We herein revealed that the crystal structure of the intracellular region of PTPRZ (PTPRZ-ICR) showed the \"head-to-toe\"-type dimer conformation, with D2 masking the catalytic site of D1. Mass spectrometry (MS) revealed that PTPRZ-ICR proteins remained in monomer-dimer equilibrium in aqueous solution, and a substrate-derived inhibitory peptide or competitive inhibitor (SCB4380) specifically bound to the monomer form in a 1:1 stoichiometric ratio, supporting the \"head-to-toe dimerization\" model for inactivation. A D2 deletion ({Delta}D2) or dimer interface mutation (DDKK) disrupted dimer formation, while the binding of SCB4380 was maintained. Similar to wild-type PTPRZ-B, monomer-biased PTPRZ-B-{Delta}D2 and PTPRZ-B-DDKK mutants efficiently dephosphorylated p190RhoGAP at Tyr-1105 when co-expressed in BHK-21 cells. The catalytic activities of these mutants were not suppressed by a treatment with PTN, but were inhibited by the cell-permeable PTPase inhibitor NAZ2329. The PTN treatment did not enhance OPC differentiation in primary cultured glial cells prepared from {Delta}D2 or catalytically-inactive CS mutant knock-in mice. Our results indicate that PTN-induced PTPRZ inactivation is attained by dimer formation of the intracellular tandem PTP domains in the head-to-toe configuration, which is physiologically relevant to the control of OPC differentiation in vivo.

biochemistry↗

bioRxiv2019

De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits

Discovery of false-positive target binding, due to assay interference or aggregation, presents a significant problem for drug discovery programs. These issues may often be unrealized and could lead researchers astray if not subject to independent verification of reproducibility and/or on-target mechanism of action. Although well-documented for small molecules, this issue has not been widely explored for peptide modality. As a case study, we demonstrate that two purported KRas inhibitors, stapled peptide SAH-SOS1A and macrocyclic peptide cyclorasin 9A5, exemplify false-positive molecules - both in terms of their sub-micromolar KRas binding affinities and their on-target cellular activities. We observed that the apparent binding of fluorescein-labeled SAH-SOS1A given by a fluorescence polarization assay is sensitive to detergent. False-positive readouts can arise from peptide adsorption to the surface of microplates. Hence, we used surface plasmon resonance and isothermal titration calorimetry to unambiguously show that both SAH-SOS1A and cyclorasin 9A5 are non-binders for KRas. Thermal shift assay and hydrogen-deuterium exchange mass spectrometry further demonstrate that both peptides destabilize KRas and induce unfolding of the protein. Furthermore, both peptides caused significant release of intracellular lactate dehydrogenase, suggesting that membrane rupture rather than on-target activity is accountable for their reported cytotoxicity. Finally, both peptides exhibited off-target activities by inhibiting the proliferation of U-2 OS and A549 cells, despite their independency of the KRas signaling pathway. Our findings demonstrate the critical need to employ orthogonal binding assays and cellular counter-screens to de-risk false-positive molecules. More rigorous workflows should lead to improved data and help obviate inadvertent scientific conclusions.\n\nSignificance statementFalse positive molecule hits occur frequently in high-throughput screens and can contaminate the scientific literature. This has become an increasingly serious issue in small molecule drug discovery and chemical probe development and it is not surprising that peptides may be similarly prone to assay interference. Using KRas as a target and two known macrocyclic peptide inhibitors as a case study, we clearly show that reporter-free biophysical assays and cellular counter-screens offer the solution to detect and de-risk the potential of false-positive compounds. We further discuss the advantages, limitations and overall strategic importance of such methods.

biochemistry↗