Turn Of Helix Research Articles

GPU-accelerated event reconstruction for the COMET Phase-I experiment

This paper discusses a parallelized event reconstruction of the COMET Phase-I experiment. The experiment aims to discover charged lepton flavor violation by observing 104.97 MeV electrons from neutrinoless muon-to-electron conversion in muonic atoms. The event reconstruction of electrons with multiple helix turns is a challenging problem because hit-to-turn classification requires a high computation cost. The introduced algorithm finds an optimal seed of position and momentum for each turn partition by investigating the residual sum of squares based on distance-of-closest-approach (DCA) between hits and a track extrapolated from the seed. Hits with DCA less than a cutoff value are classified for the turn represented by the seed. The classification performance was optimized by tuning the cutoff value and refining the set of classified hits. The workload was parallelized over the seeds and the hits by defining two GPU kernels, which record track parameters extrapolated from the seeds and finds the DCAs of hits, respectively. A reasonable efficiency and momentum resolution was obtained for a wide momentum region which covers both signal and background electrons. The event reconstruction results from the CPU and GPU were identical to each other. The benchmarked GPUs had an order of magnitude of speedup over a CPU with 16 cores while the exact speed gains varied depending on their architectures.

A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding.

SUMMARYPredicting where transcription factors bind in the genome from their in vitro DNA-binding affinity is confounded by the large number of possible interactions with nearby transcription factors. To characterize the in vivo binding logic for the Wnt effector Tcf7l2, we developed a high-throughput screening platform in which thousands of synthesized DNA phrases are inserted into a specific genomic locus, followed by measurement of Tcf7l2 binding by DamID. Using this platform at two genomic loci in mouse embryonic stem cells, we show that while the binding of Tcf7l2 closely follows the in vitro motif-binding strength and is influenced by local chromatin accessibility, it is also strongly affected by the surrounding 99 bp of sequence. Through controlled sequence perturbation, we show that Oct4 and Klf4 motifs promote Tcf7l2 binding, particularly in the adjacent ~50 bp and oscillating with a 10.8-bp phasing relative to these cofactor motifs, which matches the turn of a DNA helix.

A quantitative binding model for the Apl protein, the dual purpose recombination-directionality factor and lysis-lysogeny regulator of bacteriophage 186.

The Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl's repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.

Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates

sBackgroundTc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood.ResultsHere, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals—even mammals—and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix–turn–helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2–7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29–56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains.ConclusionsThis is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.

The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study.

Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents, such as ionization radiation. In this paper, the electronic properties of single, tandem, and clustered DNA damage in comparison with native ds-DNA are discussed as a comparative analysis for the first time. A single lesion—8-oxo-7,8-dihydro-2′-deoxyguanosine (Goxo), a tandem lesion—(5′S) and (5′R) 5′,8-cyclo-2′-deoxyadenosine (cdA), and the presence of both of them in one helix turn as clustered DNA damage were chosen and taken into consideration. The lowest vertical and adiabatic potential (VIP ~ 5.9 and AIP ~ 5.5 eV, respectively) were found for Goxo, independently of the discussed DNA lesion type and their distribution within the double helix. Moreover, the VIP and AIP were assigned for ds-trimers, ds- dimers and single base pairs isolated from parental ds-hexamers in their neutral and cationic forms. The above results were confirmed by the charge and spin density population, which revealed that Goxo can be considered as a cation radical point of destination independently of the DNA damage type (single, tandem, or clustered). Additionally, the different influences of cdA on the charge transfer rate were found and discussed in the context of tandem and clustered lesions. Because oligonucleotide lesions are effectively produced as a result of ionization factors, the presented data in this article might be valuable in developing a new scheme of anticancer radiotherapy efficiency.

Coupling of Ca2+ and voltage activation in BK channels through the αB helix/voltage sensor interface

Large-conductance Ca2+ and voltage-activated K+ (BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is composed of a voltage sensor domain (VSD), a central pore-gate domain, and a large cytoplasmic domain (CTD) that contains the Ca2+ sensors. While it is known that BK channels are activated by voltage and Ca2+, and that voltage and Ca2+ activations interact, less is known about the mechanisms involved. We explore here these mechanisms by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the Horrigan, Cui, and Aldrich model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca2+ activation for both Ca2+ bowl and RCK1 Ca2+ sites, suggesting that both high-affinity Ca2+ sites transduce their effect, at least in part, through the αB helix. Mg2+ activation also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to wild type, without other notable differences in the CTD, indicating that structural changes from the mutation were confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca2+ binding and voltage depolarization to pore opening and that shared Ca2+ and voltage transduction pathways involving the αB helix may be involved.

Direct observation of helicase–topoisomerase coupling within reverse gyrase

Reverse gyrases (RGs) are the only topoisomerases capable of generating positive supercoils in DNA. Members of the type IA family, they do so by generating a single-strand break in substrate DNA and then manipulating the two single strands to generate positive topology. Here, we use single-molecule experimentation to reveal the obligatory succession of steps that make up the catalytic cycle of RG. In the initial state, RG binds to DNA and unwinds ∼2 turns of the double helix in an ATP-independent fashion. Upon nucleotide binding, RG then rewinds ∼1 turn of DNA. Nucleotide hydrolysis and/or product release leads to an increase of 2 units of DNA writhe and resetting of the enzyme, for a net change of topology of +1 turn per cycle. Final dissociation of RG from DNA results in rewinding of the 2 turns of DNA that were initially disrupted. These results show how tight coupling of the helicase and topoisomerase activities allows for induction of positive supercoiling despite opposing torque.

In silico identification, characterization and expression profile of WUSCHEL-related homeobox (WOX) gene family in Vanilla planifolia

Vanilla planifolia is an economically important orchid, which is being commercially exploited by the food industry for the highly valued secondary metabolite vanillin. WUSCHEL-related homeobox (WOX) gene family encodes for WUSCHEL-related homeobox (WOX) transcription factors that participate in embryogenesis, organogenesis and florigenesis and in diverse plant developmental processes as well. In the present study, we analysed V. planifolia transcriptome and identified 6 WOX (VpWOX) transcripts, that encode putative WOX (VpWOX) transcription factor proteins. Domain analysis was done which indicates the presence of helix-loop-helix-turn-helix which is identifying feature of WOX gene family proteins. We executed phylogenetic clustering for the VpWOX proteins with their counterpart from the model plant Arabidopsis thaliana (AtWOX) and other closely related orchid species, Phalaenopsis equestris (PeWOX), Dendrobium catenatum (DcWOX) and Apostasia shenzhenica (AsWOX) and established their clade specific grouping. Spatio-temporal expression profile for VpWOX genes was analysed for different plant developmental stages which shows that VpWOX13 is expressing uniformly in all the developmental stages whereas, other genes have tissue specific expression. Based on gene expression patterns, we selected four VpWOX proteins and carried out secondary and tertiary structural analysis which indicates the presence of alpha helix and beta turn in the protein structure. The present study provides basic understanding of the functioning of WOX gene family in V. planifolia and paves the path for functional characterization of selected VpWOX genes in planta and in heterologous system in future for commercial utilization.

Functional Analysis of IRF1 Reveals its Role in the Activation of the Type I IFN Pathway in Golden Pompano, Trachinotus ovatus (Linnaeus 1758).

Interferon (IFN) regulatory factor 1 (IRF1), a transcription factor with a novel helix–turn–helix DNA-binding domain, plays a crucial role in innate immunity by regulating the type I IFN signaling pathway. However, the regulatory mechanism through which IRF1 regulates type I IFN in fish is not yet elucidated. In the present study, IRF1 was characterized from golden pompano, Trachinotus ovatus (designated ToIRF1), and its immune function was identified to elucidate the transcriptional regulatory mechanism of ToIFNa3. The full-length complementary DNA (cDNA) of IRF1 is 1763 bp, including a 900-bp open reading frame (ORF) encoding a 299-amino-acid polypeptide. The putative protein sequence has 42.7–71.7% identity to fish IRF1 and possesses a representative conserved domain (a DNA-binding domain (DBD) at the N-terminus). The genomic DNA sequence of ToIRF1 consists of eight exons and seven introns. Moreover, ToIRF1 is constitutively expressed in all examined tissues, with higher levels being observed in immune-relevant tissues (whole blood, gill, and skin). Additionally, Cryptocaryon irritans challenge in vivo increases ToIRF1 expression in the skin as determined by Western blotting (WB); however, protein levels of ToIRF1 in the gill did not change significantly. The subcellular localization indicates that ToIRF1 is localized in the nucleus and cytoplasm with or without polyinosinic/polycytidylic acid (poly (I:C)) induction. Furthermore, overexpression of ToIRF1 or ToIFNa3 shows that ToIRF1 can notably activate ToIFNa3 and interferon signaling molecule expression. Promoter sequence analysis finds that several interferon stimulating response element (ISRE) binding sites are present in the promoter of ToIFNa3. Additionally, truncation, point mutation, and electrophoretic mobile shift (EMSA) assays confirmed that ToIRF1 M5 ISRE binding sites are functionally important for ToIFNa3 transcription. These results may help to illuminate the roles of teleost IRF1 in the transcriptional mechanisms of type I IFN in the immune process.

NMR Structure of the FIV gp36 C-Terminal Heptad Repeat and Membrane-Proximal External Region.

Feline immunodeficiency virus (FIV), a lentivirus causing an immunodeficiency syndrome in cats, represents a relevant model of pre-screening therapies for human immunodeficiency virus (HIV). The envelope glycoproteins gp36 in FIV and gp41 in HIV mediate the fusion of the virus with the host cell membrane. They have a common structural framework in the C-terminal region that includes a Trp-rich membrane-proximal external region (MPER) and a C-terminal heptad repeat (CHR). MPER is essential for the correct positioning of gp36 on the lipid membrane, whereas CHR is essential for the stabilization of the low-energy six-helical bundle (6HB) that is necessary for the fusion of the virus envelope with the cell membrane. Conformational data for gp36 are missing, and several aspects of the MPER structure of different lentiviruses are still debated. In the present work, we report the structural investigation of a gp36 construct that includes the MPER and part of the CHR domain (737-786gp36 CHR–MPER). Using 2D and 3D homo and heteronuclear NMR spectra on 15N and 13C double-labelled samples, we solved the NMR structure in micelles composed of dodecyl phosphocholine (DPC) and sodium dodecyl sulfate (SDS) 90/10 M: M. The structure of 737-786gp36 CHR–MPER is characterized by a helix–turn–helix motif, with a regular α-helix and a moderately flexible 310 helix, characterizing the CHR and the MPER domains, respectively. The two helices are linked by a flexible loop regulating their orientation at a ~43° angle. We investigated the positioning of 737-786gp36 CHR–MPER on the lipid membrane using spin label-enhanced NMR and ESR spectroscopies. On a different scale, using confocal microscopy imaging, we studied the effect of 737-786gp36 CHR–MPER on 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-(1’-rac-glycerol) (DOPC/DOPG) multilamellar vesicles (MLVs). This effect results in membrane budding and tubulation that is reminiscent of a membrane-plasticizing role that is typical of MPER domains during the event in which the virus envelope merges with the host cell membrane.

A thermophilic phage uses a small terminase protein with a fixed helix–turn–helix geometry

Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerSP76-26 revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerSP76-26 to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerSP76-26, revealing key differences between this thermophilic phage and its mesophilic counterparts.

Regulation of aureofuscin production by the PAS-LuxR family regulator AurJ3M

aurJ3M(GenBank:EU697915.1), a 579 bp gene, whose deduced product (192 amino acid) was found to have amino acid sequence homology with some bacterial regulatory proteins. Computer-assisted analysis showed that AurJ3M is PAS-LuxR family regulatory protein, it combines a PAS domain with a helix–turn–helix (HTH) motif of the LuxR type. Gene deletion of aurJ3M from the S.aureofuscus SYAU0709 through gene replacement with the apramycin resistance gene aac (3) IV and the DNA fragment of the replication initiation site sequence OriT resulted in complete loss of aureofuscin production, indicating that AurJ3M is a positive regulator during the aureofuscin biosynthesis.Gene expression analyses in S.aureofuscus SYAU0709 and S.aureofuscus ΔaurJ3M by reverse transcriptase PCR (RT-PCR) indicated there no transcripts for the genes B、C、G、F、S0、S1、D in S.aureofuscus ΔaurJ3M, maintains some transcription of these genes although the levels is low. Transcription was also significantly reduced for gene A, and no difference in the transcription pattern was observed for the genes R、E and H, a similar transcription pattern was also observed for AurJ3M, A and B showed a different transcription pattern, while transcription of gene A in S.aureofuscus ΔaurJ3M when compared to the parental strain, no transcripts could be detected for gene B in the mutant; This result indicates that the deletion of aurJ3M gene doesn't have a polar effect on the transcription of genes located downstream from aurJ3M. In the ΔaurJ3M knockout mutant, except for the transcription of E、H、M and R, the transcription of other genes in the cluster was down-regulated, HPLC shows there no secondary metabolites was produced,aurJ3M has a pathway-specific regulation effect on the biosynthesis of aureofuscin. Aureofuscin had broad application prospects in food preservation, and enriched the resource pool of anti-fungal antibiotics of tetraphenyl macrolide in China.

The Energy Landscape of Voltage Sensing in Ci-VSP

The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane associated phosphatidylinositol lipid phosphatase. The enzymatic activity of the cytoplasmic phosphatase domain is directly regulated by changes in the transmembrane electric field through conformational rearrangements at the voltage-sensing domain (VSD). Ci-VSD shares high sequence and structural similarity with the VSD of voltage-gated cation and proton channels, and is the only membrane-spanning domain of Ci-VSP. Previously, we have determined the structure of Ci-VSD in its resting (Down) and activated (Up) conformations. Thus, this system provides us with a great opportunity to study the energetics of the gating mechanism of this isolated VSD. Using mutagenesis, electrophysiology, modeling and molecular dynamics simulations, we systematically investigated residue-residue interactions between the segments of the VSD and the interactions between the VSD and lipids during a complete functional gating cycle. We found that Ci-VSD can adopt mainly four conformational states: the Up and Down states determined by crystallography, in addition to a further down (‘Down-minus’) and a further up (‘Up-plus’) states. One helix turn translation of the S4 segment drives the transition between two adjacent states. Upon depolarization, the VSD rearranges from the ‘Down-minus’ state to the ‘Up-plus’ state in a sequential stepwise way, translating one positively charged residue across the membrane electric field at each transition, resulting in a gating charge of ∼3 e0. Furthermore, cysteine mutations on the extracellular side of S4 can form metal-ion bridges with lipid phosphate group and decrease the total gating charge displacement with intensity depending on the external Cd2+ concentration, while cysteine mutations on the S1−S3 segments have little effect, representing minor conformational changes of them during gating and do not contribute to the gating charge.

Analysis and Reduction of Detent Effect in Magnetic Lead Screws With Parallel Magnetized Permanent Magnet Segments

This paper deals with the analysis and suppression of detent effect in the magnetic lead screw (MLS), which is equipped with parallel magnetized permanent magnet (PM) segments to approximate the helical PM for manufacturing simplicity. The detent effect is caused by the non-uniform magnetization along the helical PM, and behaves as both thrust force ripple and torque ripple during the transmission process. In this paper, a three-dimensional (3-D) analytical model of the MLS is established to analyze and predict the air-gap magnetic field, and the thrust force and torque are then derived, as well as their ripple components. It demonstrates that the harmonic order of the ripples is solely dependent on PM segments' quantities per helix turn on both the nut and screw. The analytical analysis is verified by extensive 3-D numerical computations. The impact of load angel and quantities of PM segments on the detent effect are investigated. It's shown that the torque ripple suffers more seriously than thrust force ripple, and both ripple percentages drop with the increase of load angle. And it is highlighted that larger least common multiple of PM segments' quantities on screw and nut is conducive to improving the average values of thrust force and torque, and reducing the detent effect.

HIV Capsid and Protease, New Targets of Melittin

Melittin is a 26 amino acid amphipathic peptide, the main part of a bee venom. It has been confirmed that melittin can act against a vast verity of infectious agents, such as human immunodeficiency virus (HIV). This study aimed to investigate all physicochemical properties, post-modification sites, and interactions between melittin and HIV proteins. Ten Melittin sequences from different honey bees were collected from NCBI genebank. The physicochemical properties were evaluated for all sequences, and phosphorylation sites, glycolization positions and disulfide bonds were determined. Signal peptide was predicted by SignalP, secondary and tertiary structures were constructed by different software. Docking and interaction analysis were done by HEX and Discovery Studio. Results showed that most mutations occurred in Apis florae; this genotype was placed in a district clade in the cladogram. Physicochemical features showed melittin to be a basic protein and stable in prokaryotic and eukaryotic cells. It is an allergen peptide and no disulfide bonds and glycosylation site was found in its structure. Just one phosphorylation position was found and the majority of secondary structures are Alpha helix and Beta turn. High energy values of interactions belonged to capsid and protease proteins, and docking showed several amino acids to be involved in the interactions. Our observations suggested that in addition to envelope and long terminal repeat, capsid and proteases of HIV could have a great potential as a target for melittin. Our data provides a comprehensive understanding of melittin properties, structures, and its interaction with HIV proteins.

Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach.

Dehydrodolichyl diphosphate synthase (DHDDS) is the catalytic subunit of the heteromeric human cis-prenyltransferase complex, synthesizing the glycosyl carrier precursor for N-linked protein glycosylation. Consistent with the important role of N-glycosylation in protein biogenesis, DHDDS mutations result in human diseases. Importantly, DHDDS encompasses a C-terminal region, which does not converge with any known conserved domains. Therefore, despite the clinical importance of DHDDS, our understating of its structure–function relations remains poor. Here, we provide a structural model for the full-length human DHDDS using a multidisciplinary experimental and computational approach. Size-exclusion chromatography multi-angle light scattering revealed that DHDDS forms a monodisperse homodimer in solution. Enzyme kinetics assays revealed that it exhibits catalytic activity, although reduced compared to that reported for the intact heteromeric complex. Our model suggests that the DHDDS C-terminus forms a helix–turn–helix motif, tightly packed against the core catalytic domain. This model is consistent with small-angle X-ray scattering data, indicating that the full-length DHDDS maintains a similar conformation in solution. Moreover, hydrogen–deuterium exchange mass-spectrometry experiments show time-dependent deuterium uptake in the C-terminal domain, consistent with its overall folded state. Finally, we provide a model for the DHDDS–NgBR heterodimer, offering a structural framework for future structural and functional studies of the complex.

FLOWERING HTH1 is involved in CONSTANS-mediated flowering regulation in Arabidopsis

Flowering at the right time is essential for maximum reproductive fitness. In Arabidopsis thaliana, the CONSTANS (CO) protein facilitates the transition from the vegetative phase to the reproductive phase under long-day conditions. The formation of heterodimeric complexes between CO and DNA binding domain-containing transcription factors is important for the induction of day length-dependent flowering. Here, we report a myb-like helix turn helix (HTH) transcriptional regulator family protein as a new modulator of floral transition, which we have named FLOWERING HTH1 (FHTH1). We isolated FHTH1 as a CO-interacting protein by a yeast two-hybrid screen using an Arabidopsis transcription factor library. Our analysis showed that FHTH1 presented in the nucleus and the FHTH1-CO complex was formed in the same subcellular location. We also observed the expression of a FHTH1:GUS construct in the leaf vasculature, where CO exists. Transgenic plants overexpressing FHTH1 fused with the plant-specific repression domain SRDX showed a delayed flowering phenotype in long days, resembling the phenotype of the co mutant. Our results suggest that FHTH1 may contribute to CO-mediated photoperiodic flowering regulation.

Helical antiferromagnetic ordering in EuNi1.95As2 single crystals

The Eu{+2} spins-7/2 in EuNi2As2 with the body-centered tetragonal ThCr2Si2 structure order antiferromagnetically below the Neel temperature TN =15 K into a helical antiferromagnetic (AFM) structure with the helix axis aligned along the tetragonal c axis and the Eu ordered moments aligned ferromagnetically within the ab plane as previously reported from neutron diffraction measurements [T. Jin, et al., Phys. Rev. B 99, 014425 (2019)]. Here we study the crystallographic, magnetic, thermal, and electronic transport properties of Bi-flux-grown single crystals using single-crystal x-ray diffraction, anisotropic magnetic susceptibility chi, isothermal magnetization M, heat capacity Cp, and electrical resistivity rho measurements versus applied magnetic field H and temperature T. Vacancies are found on the Ni sites corresponding to the composition EuNi{1.95}As2. The chi{ab}(T) data below TN are fitted well by molecular field theory (MFT), and the helix turn angle kd and the Eu-Eu Heisenberg exchange constants are extracted from the fit parameters. The kd value is in good agreement with the neutron-diffraction result. The magnetic contribution to the zero-field heat capacity below TN is also fitted by MFT. The isothermal in-plane magnetization Mab exhibits two metamagnetic transitions versus H, whereas Mc(T = 2 K) is nearly linear up to H =14 T, both behaviors being consistent with MFT. The Mc(H,T), rho(Hc,T), and Cp(Hc,T) data yielded a Hc-T phase diagram separating the AFM and paramagnetic phases in good agreement with MFT. Anisotropic chi(T) literature data for the ThCr2Si2-type helical antiferromagnet EuRh2As2 are also fitted well by MFT. A comparison is made between the crystallographic and magnetic properties of ThCr2Si2- type EuM2Pn2 compounds with M = Fe, Co, Ni, Cu, or Rh, and Pn = P or As, where only ferromagnetic and c-axis helical AFM structures are found.

Folding and Assembly of Short α, β, γ-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures.

Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible, and peptides 2a and 2b adopt a noncanonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. The revealed systems offer ample opportunity for further structural optimization and applications.

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. Here we have used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We have found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple, regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix) characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high affinity binding but is essential for specificity. Finally, we find that Satb1-DNA interactions are mechanosensitive. Increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.