scholarly journals Computationally-guided tuning of ligand sensitivity in a GPCR-based sensor

2021 ◽  
Author(s):  
Daniel Keri ◽  
Reto B. Cola ◽  
Kagiampaki Zacharoula ◽  
Tommaso Patriarchi ◽  
Patrick Barth

Genetically-encoded fluorescent sensors for neuromodulators are increasingly used molecular tools in neuroscience. However, these protein-based biosensors are often limited by the sensitivity of the protein scaffold towards endogenous ligands. Here, we explored the possibility of applying computational design approaches for enhancing sensor sensitivity. Using the dopamine sensor dLight1 as proof of concept, we designed two variants that boost the sensor's potency (EC50) for dopamine and norepinephrine by up to 5- and 15-fold, respectively. Interestingly, the largest effects were obtained through improved designed allosteric transmission in the transmembrane region of the sensor. Our approach should prove generally useful for enhancing sensing capabilities of a large variety of neuromodulator sensors.

2019 ◽  
Vol 1 (5) ◽  
pp. 1833-1846 ◽  
Author(s):  
Santiago Sosa ◽  
Andrés H. Rossi ◽  
Alan M. Szalai ◽  
Sebastián Klinke ◽  
Jimena Rinaldi ◽  
...  

In this work we rationally redesign and engineer a decameric protein scaffold to generate an asymmetric Janus-like protein nanoparticle. As a proof of concept this novel scaffold is functionalized (i) to fluorescently label eukaryotic cells and (ii) to generate a multichromophoric FRET nanoparticle.


2017 ◽  
Vol 53 (54) ◽  
pp. 7604-7607 ◽  
Author(s):  
Xiaoqiang Huang ◽  
Jing Xue ◽  
Yushan Zhu

A new protein scaffold was identified and redesigned to catalyze the synthesis of β-lactam antibiotic cephradine.


2018 ◽  
Author(s):  
Joshua Rees ◽  
Oliver Chalkley ◽  
Sophie Landon ◽  
Oliver Purcell ◽  
Lucia Marucci ◽  
...  

AbstractIn the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay, the cell either replicates or not. We used the first (and currently only published) whole-cell model, for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in-silico minimal genomes smaller than JCVI-Syn3.0, a bacteria with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essentiality genes, 18 high essentiality genes, and produced evidence for at least two Mycoplasma genitalium in-silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer.


2018 ◽  
Author(s):  
Noah Jakimo ◽  
Pranam Chatterjee ◽  
Joseph M Jacobson

RNA and DNA profiles can help classify a variety of biological states, including disease, metabolism and cell type. In a proof-of-concept study on novel genetically encodable components for detecting single-stranded oligonucleotides, we engineered switchable CRISPR guide RNA (swigRNA) with Cas9 affinity that is conditional on sensing an oligo trigger molecule (trigRNA or trigDNA). RNA- and DNA-sensing swigRNAs that serve as off-to-on and on-to-off switches for Cas9 cleavage were achieved by computational design of hybridization dependencies in the guide. This study highlights functional swigRNA structures that implement toehold-gated strand-displacement with their triggers, and should merit further engineering and kinetic characterization.


2021 ◽  
Author(s):  
Jérôme G. Prunier ◽  
Géraldine Loot ◽  
Charlotte Veyssiere ◽  
Nicolas Poulet ◽  
Simon Blanchet

ABSTRACTRivers are heavily fragmented by man-made instream barriers such as dams and weirs. This hyper-fragmentation is a major threat to freshwater biodiversity and restoration policies are now adopted worldwide to mitigate these impacts. However, there is surprisingly little feedback on the efficiency of barrier mitigation measures in restoring riverine connectivity, notably for non-migratory fish species. Here, we implemented a “before-after genetic monitoring” of the restoration of 11 weirs in France using a dedicated genetic index of fragmentation (the FINDEX), with a focus on five fish species from two genera. We found that most obstacles actually had a significant impact on connectivity before restoration, especially the highest and steepest ones, with an overall barrier effect of about 51% of the maximal theoretical impact. Most importantly, we demonstrated for the first time that mitigation measures such as dam removal or fish pass creation significantly and rapidly improved connectivity, with –for some barriers-a complete recovery of the genetic connectivity in less than twelve months. Our study provides a unique and strong proof-of-concept that barrier removal is an efficient strategy to restore riverine connectivity and that molecular tools can provide accurate measures of restoration efficiency within a few months.Graphical Abstract


Chemosensors ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 47 ◽  
Author(s):  
Eun-A Kwak ◽  
LeNaiya Kydd ◽  
Butaek Lim ◽  
Justyn Jaworski

In this study, we examine a means for developing near-IR fluorescent sensors through streamlined, site-specific coupling with peptide-based receptors. As the penultimate step of solid-phase synthesis of a peptide-based receptor, we show a simple means of labeling the N’ terminus with the near IR fluorophore IR-783 to afford a viable fluorescent sensor after cleavage from the resin. The proof-of-concept probe utilized a biotin mimetic peptide sequence as the receptive moiety. Here we revealed a “turn-on” fluorescence enhancement upon binding of the biotin mimetic probe to its intended streptavidin target. Not all peptide-receptive moieties tested were able to generate such an enhancement upon target binding, and as such, the rationale for the observed fluorescence response properties is discussed.


2019 ◽  
Vol 25 (44) ◽  
pp. 10350-10358
Author(s):  
Siyuan Li ◽  
Wanjia Xu ◽  
Shengnan Chu ◽  
Ningning Ma ◽  
Shengda Liu ◽  
...  

Genetics ◽  
2020 ◽  
Vol 216 (4) ◽  
pp. 947-956
Author(s):  
Ziduan Han ◽  
Wen-Sui Lo ◽  
James W. Lightfoot ◽  
Hanh Witte ◽  
Shuai Sun ◽  
...  

A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.


Author(s):  
A. G. Jackson ◽  
M. Rowe

Diffraction intensities from intermetallic compounds are, in the kinematic approximation, proportional to the scattering amplitude from the element doing the scattering. More detailed calculations have shown that site symmetry and occupation by various atom species also affects the intensity in a diffracted beam. [1] Hence, by measuring the intensities of beams, or their ratios, the occupancy can be estimated. Measurement of the intensity values also allows structure calculations to be made to determine the spatial distribution of the potentials doing the scattering. Thermal effects are also present as a background contribution. Inelastic effects such as loss or absorption/excitation complicate the intensity behavior, and dynamical theory is required to estimate the intensity value.The dynamic range of currents in diffracted beams can be 104or 105:1. Hence, detection of such information requires a means for collecting the intensity over a signal-to-noise range beyond that obtainable with a single film plate, which has a S/N of about 103:1. Although such a collection system is not available currently, a simple system consisting of instrumentation on an existing STEM can be used as a proof of concept which has a S/N of about 255:1, limited by the 8 bit pixel attributes used in the electronics. Use of 24 bit pixel attributes would easily allowthe desired noise range to be attained in the processing instrumentation. The S/N of the scintillator used by the photoelectron sensor is about 106 to 1, well beyond the S/N goal. The trade-off that must be made is the time for acquiring the signal, since the pattern can be obtained in seconds using film plates, compared to 10 to 20 minutes for a pattern to be acquired using the digital scan. Parallel acquisition would, of course, speed up this process immensely.


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