Abstract:
:Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here the Escherichia coli RbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in an E. coli reporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2-1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Tavares D,Reimer A,Roy S,Joublin A,Sentchilo V,van der Meer JRdoi
10.1038/s41598-019-53507-5subject
Has Abstractpub_date
2019-11-15 00:00:00pages
16940issue
1issn
2045-2322pii
10.1038/s41598-019-53507-5journal_volume
9pub_type
杂志文章abstract::Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep44447
更新日期:2017-03-14 00:00:00
abstract::Successful tick feeding is facilitated by an assortment of pharmacologically-active factors in tick saliva that create an immunologically privileged micro-environment in the host's skin. Through a process known as saliva-assisted transmission, bioactive tick salivary factors modulate the host environment, promoting tr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-49572-5
更新日期:2019-09-11 00:00:00
abstract::In this study we analysed the acoustic properties and presence of haddock calls in the Arctic fjord Kongsfjorden (79° N-12° E, Svalbard Islands, Norway) in one year. Data were collected with three autonomous acoustic recorders located in the inner, middle, and outer parts of the fjord. The fjord is characterized by a ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-75415-9
更新日期:2020-10-26 00:00:00
abstract::Ultraviolet-B (UVB) radiation damages plants and decreases their growth and productivity. We previously demonstrated that UVB sensitivity varies widely among Asian rice (Oryza sativa L.) cultivars and that the activity of cyclobutane pyrimidine dimer (CPD) photolyase, which repairs UVB-induced CPDs, determines UVB sen...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-59720-x
更新日期:2020-02-21 00:00:00
abstract::In mature erythrocytes, glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) yield NADPH, a crucial cofactor of the enzyme glutathione reductase (GR) converting glutathione disulfide (GSSG) into its reduced state (GSH). GSH is essential for detoxification processes in and survival of ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep28754
更新日期:2016-06-29 00:00:00
abstract::Low level light therapy receives increasing interest in the fields of tissue regeneration and wound healing. Several in vivo studies demonstrated the positive effects of LLLT on angiogenesis. This study aimed to investigate the underlying properties in vitro by comparing the effects of light therapy by light emitting ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-11061-y
更新日期:2017-09-06 00:00:00
abstract::Despite being a cardinal experimental model, the induction of cirrhosis in rats by repeated exposure to carbon tetrachloride (CCl4) has low reproducibility. Here, we compared two models of cirrhosis induced by orogastric administration of CCl4 once (CCl4-1xWk) or twice a week (CCl4-2xWk) for 12 weeks in male Sprague-D...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-27427-9
更新日期:2018-06-15 00:00:00
abstract::The largest tsunamis are generated by seafloor uplift resulting from rupture of offshore subduction-zone megathrusts. The rupture of the shallowest part of a megathrust often produces unexpected outsize tsunami relative to their seismic magnitude. These are so called 'tsunami earthquakes', which are difficult to ident...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-68097-w
更新日期:2020-07-06 00:00:00
abstract::Atomoxetine is a norepinephrine reuptake inhibitor indicated in the treatment of attention-deficit/hyperactivity disorder. It is primarily metabolized by CYP2D6 to its equipotent metabolite, 4-hydroxyatomoxetine, which promptly undergoes further glucuronidation to an inactive 4-HAT-O-glucuronide. Clinical trials have ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-30841-8
更新日期:2018-08-17 00:00:00
abstract::Powdered activated carbon (AC) is commonly used as an effective additive to enhance anaerobic digestion (AD), but little is known about how the metabolic pathways resulting from adding AC change the microbial association network and enhance food waste treatment. In this work, the use of AC in an anaerobic digestion sy...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-11826-5
更新日期:2017-09-12 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Scientific reports
pub_type: 已发布勘误
doi:10.1038/s41598-020-58144-x
更新日期:2020-01-21 00:00:00
abstract::Effects of fertilisation and other management techniques on a weed community were evaluated during wheat growth in a rice-wheat cropping system. Fertiliser treatments were C0 (C means chemical, C0 means zero chemical fertiliser.), CN (N fertiliser), CNK (N plus K fertiliser), CNPK (N plus P and K fertiliser), CNP (N p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-22389-4
更新日期:2018-03-05 00:00:00
abstract::Hepatic stellate cells (HSCs) known as "master producers" and macrophages as "master regulators", are the key cell types that strongly contribute to the progression of liver fibrosis. Since Notch signaling regulates multiple cellular processes, we aimed to study the role of Notch signaling in HSCs differentiation and ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep18272
更新日期:2015-12-14 00:00:00
abstract::Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living spec...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep46487
更新日期:2017-04-19 00:00:00
abstract::Climate warming is likely to interact with other stressors to challenge the physiological capacities and survival of phenotypes within populations. This may be especially true for the billions of fishes per year that undergo vigorous exercise prior to escaping or being intentionally released from fishing gear. Using a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep40571
更新日期:2017-01-17 00:00:00
abstract::State-of-art quantum key distribution (QKD) systems are performed with several GHz pulse rates, meanwhile privacy amplification (PA) with large scale inputs has to be performed to generate the final secure keys with quantified security. In this paper, we propose a fast Fourier transform (FFT) enhanced high-speed and l...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-50290-1
更新日期:2019-10-31 00:00:00
abstract::The accelerated discovery of disease-related genes emerging from genomic studies has strained the capacity of traditional genetically engineered mouse models (GEMMs) to provide in-vivo validation. Direct, somatic, genetic engineering approaches allow for accelerated and flexible genetic manipulation and represent an a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep11061
更新日期:2015-06-05 00:00:00
abstract::Non-functioning pituitary adenomas (NFPAs) are the most frequent pituitary tumors. The elucidation of the mechanisms of aggressive NFPAs in bone destruction is required in order to guide the clinical diagnosis and treatment of NFPAs. In the present study, we investigated the differential proteomics of fibroblasts isol...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-17679-2
更新日期:2017-12-13 00:00:00
abstract::The interfacial Dzyaloshinskii-Moriya interaction (DMI) is an essential ingredient for stabilizing chiral spin configurations in spintronic applications. Here, via first-principles calculations, we reveal the influence of lattice strain on DMI in Co/Pt interface. We observed a considerable enhancement for a certain la...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-69360-w
更新日期:2020-07-23 00:00:00
abstract::To enhance the carbon dioxide (CO2) uptake of metal-organic frameworks (MOFs), amine functionalization of their pore surfaces has been studied extensively. In general, amine-functionalized MOFs have been synthesized via post-synthetic modifications. Herein, we introduce a one-step construction of a MOF ([(NiLethylamin...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep19337
更新日期:2016-01-13 00:00:00
abstract::Resistance to adjuvant systemic treatment, including taxanes (docetaxel and paclitaxel) is a major clinical problem for breast cancer patients. lncRNAs (long non-coding RNAs) are non-coding transcripts, which have recently emerged as important players in a variety of biological processes, including cancer development ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-36231-4
更新日期:2018-12-19 00:00:00
abstract::Transforming growth factor β-1 (TGFβ-1)-induced phosphorylation of transcription factors Smad2 and Smad3 plays a crucial role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the molecular regulation of Smad2/Smad3 proteins stability remains a mystery. Here, we show that ubiquitin carboxyl-terminal...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep33116
更新日期:2016-09-08 00:00:00
abstract::Widely regarded as an imminent threat to our oceans, ocean acidification has been documented in all oceanic basins. Projected changes in seawater chemistry will have catastrophic biotic effects due to ocean acidification hindering biogenic carbonate production, which will in turn lead to substantial changes in marine ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-58501-w
更新日期:2020-01-31 00:00:00
abstract::We address the impact of the spin-orbit (SO) coupling on the localization-delocalization-transition (LDT) in a spin-orbit coupled Bose-Einstein condensate in a bichromatic potential. We find that SO coupling significantly alters the threshold depth of the one of sublattices above which the lowest eigenstates transform...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep31700
更新日期:2016-08-17 00:00:00
abstract::Nitric oxide synthase like enzyme (NOS-like enzyme), which produces nitric oxide, participates in many biological processes. However it remains unidentified and highly controversial that plants do possess a NOS-like enzyme. In this paper, a novel arginine analogue NP1 was designed and developed for the direct identifi...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep32630
更新日期:2016-09-02 00:00:00
abstract::Controlling thickness and tightness of surface passivation shells is crucial for many applications of core-shell nanoparticles (NP). Usually, to determine shell thickness, core and core/shell particle are measured individually requiring the availability of both nanoobjects. This is often not fulfilled for functional n...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-77530-z
更新日期:2020-11-26 00:00:00
abstract::Galectin-3 is a biomarker of fibrosis, inflammation and oxidative stress, and its role in heart remodelling and exercise intolerance has not been conclusively proven in heart failure (HF) patients with reduced ejection fraction (rEF). We prospectively assessed 67 consecutive patients with symptomatic HF and left ventr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-73634-8
更新日期:2020-10-07 00:00:00
abstract::The role of soil organic carbon in global carbon cycles is receiving increasing attention both as a potentially large and uncertain source of CO2 emissions in response to predicted global temperature rises, and as a natural sink for carbon able to reduce atmospheric CO2. There is general agreement that the technical p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-15794-8
更新日期:2017-11-14 00:00:00
abstract::The plant hormone abscisic acid (ABA) and the jasmonic acid related-compound 12-oxo-phytodienoic acid (OPDA) play crucial roles in seed development, dormancy, and germination. However, a lack of suitable techniques for visualising plant hormones has restricted the investigation of their biological mechanisms. In the p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep42977
更新日期:2017-02-17 00:00:00
abstract::In this report, we demonstrate mid-infrared dual-waveband (i.e., ~3 μm and ~2 μm) pulses from a cascaded gain-switched Ho3+-doped ZBLAN fiber laser by the use of hybrid pumping of 1150 nm CW and pulse LDs for the first time. Stable ~3 μm gain-switched pulses with the maximum output power 262.14 mW and shortest pulse d...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-17305-1
更新日期:2017-12-04 00:00:00