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1358 Publications

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    03/21/18 | Development of a Rubredoxin-Type Center Embedded in a de Dovo-Designed Three-Helix Bundle
    Tebo AG, Pinter TB, García-Serres R, Speelman AL, Tard C, Sénèque O, Blondin G, Latour J, Penner-Hahn J, Lehnert N, Pecoraro VL
    Biochemistry. 03/2018;57:2308 – 2316. doi: 10.1021/acs.biochem.8b00091

    Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet–visible, Mössbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe(II) and Fe(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold.

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    02/20/18 | Structure of full-length human TRPM4.
    Duan J, Li Z, Li J, Santa-Cruz A, Sanchez-Martinez S, Zhang J, Clapham DE
    Proceedings of the National Academy of Sciences of the United States of America. 2018 Feb 20;115(10):2377-82. doi: 10.1073/pnas.1722038115

    Transient receptor potential melastatin subfamily member 4 (TRPM4) is a widely distributed, calcium-activated, monovalent-selective cation channel. Mutations in human TRPM4 (hTRPM4) result in progressive familial heart block. Here, we report the electron cryomicroscopy structure of hTRPM4 in a closed, Na-bound, apo state at pH 7.5 to an overall resolution of 3.7 Å. Five partially hydrated sodium ions are proposed to occupy the center of the conduction pore and the entrance to the coiled-coil domain. We identify an upper gate in the selectivity filter and a lower gate at the entrance to the cytoplasmic coiled-coil domain. Intramolecular interactions exist between the TRP domain and the S4-S5 linker, N-terminal domain, and N and C termini. Finally, we identify aromatic interactions via π-π bonds and cation-π bonds, glycosylation at an N-linked extracellular site, a pore-loop disulfide bond, and 24 lipid binding sites. We compare and contrast this structure with other TRP channels and discuss potential mechanisms of regulation and gating of human full-length TRPM4.

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    01/08/18 | Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity
    Koebke KJ, Yu F, Salerno E, Stappen CV, Tebo AG, Penner-Hahn JE, Pecoraro VL
    Angewandte Chemie International Edition. 01/2018;57:3954 – 3957. doi: 10.1002/anie.201712757

    Protein design is a useful strategy to interrogate the protein structure‐function relationship. We demonstrate using a highly modular 3‐stranded coiled coil (TRI‐peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H2O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75‐fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three‐coordinate CuI in a site, which tends toward two‐coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal‐center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.

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    Kainmueller Lab
    12/01/17 | Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
    Dye NA, Popović M, Spannl S, Etournay R, Kainmüller D, Ghosh S, Myers EW, Jülicher F, Eaton S
    Development (Cambridge, England). 2017 Dec 01;144(23):4406-4421. doi: 10.1242/dev.155069

    Quantitative analysis of the dynamic cellular mechanisms shaping the Drosophila wing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires explants to be imaged under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systems in vivo and in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to observe growth directly and to apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that whereas cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.

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    11/16/17 | Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing.
    Li H, Horns F, Wu B, Xie Q, Li J, Li T, Luginbuhl DJ, Quake SR, Luo L
    Cell. 11/2017;171(5):1206-1220.e22. doi: 10.1016/j.cell.2017.10.019

    The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes. Transcriptomes of closely related PN classes exhibit the largest differences during circuit assembly but become indistinguishable in adults, suggesting that neuronal subtype diversity peaks during development. Transcription factors and cell-surface molecules are the most differentially expressed genes between classes and are highly informative in encoding cell identity, enabling us to identify a new lineage-specific transcription factor that instructs PN dendrite targeting. These findings establish that neuronal transcriptomic identity corresponds with anatomical and physiological identity defined by connectivity and function.

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    10/17/13 | Homeostatic plasticity shapes the visual system’s first synapse
    Johnson RE, Tien N, Shen N, Pearson JT, Soto F, Kerschensteiner D
    Nature Communications. 10/2017;8(1):. doi: 10.1038/s41467-017-01332-7

    Vision in dim light depends on synapses between rods and rod bipolar cells (RBCs). Here, we find that these synapses exist in multiple configurations, in which single release sites of rods are apposed by one to three postsynaptic densities (PSDs). Single RBCs often form multiple PSDs with one rod; and neighboring RBCs share ~13% of their inputs. Rod-RBC synapses develop while ~7% of RBCs undergo programmed cell death (PCD). Although PCD is common throughout the nervous system, its influences on circuit development and function are not well understood. We generate mice in which ~53 and ~93% of RBCs, respectively, are removed during development. In these mice, dendrites of the remaining RBCs expand in graded fashion independent of light-evoked input. As RBC dendrites expand, they form fewer multi-PSD contacts with rods. Electrophysiological recordings indicate that this homeostatic co-regulation of neurite and synapse development preserves retinal function in dim light.

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    10/18/17 | Stochastic simulation of dopamine neuromodulation for implementation of fluorescent neurochemical probes in the striatal extracellular space.
    Beyene AG, McFarlane IR, Pinals RL, Landry MP
    ACS Chemical Neuroscience. 2017 Oct 18;8(10):2275-2289. doi: 10.1021/acschemneuro.7b00193

    Imaging the dynamic behavior of neuromodulatory neurotransmitters in the extracelluar space that arise from individual quantal release events would constitute a major advance in neurochemical imaging. Spatial and temporal resolution of these highly stochastic neuromodulatory events requires concurrent advances in the chemical development of optical nanosensors selective for neuromodulators in concert with advances in imaging methodologies to capture millisecond neurotransmitter release. Herein, we develop and implement a stochastic model to describe dopamine dynamics in the extracellular space (ECS) of the brain dorsal striatum to guide the design and implementation of fluorescent neurochemical probes that record neurotransmitter dynamics in the ECS. Our model is developed from first-principles and simulates release, diffusion, and reuptake of dopamine in a 3D simulation volume of striatal tissue. We find that in vivo imaging of neuromodulation requires simultaneous optimization of dopamine nanosensor reversibility and sensitivity: dopamine imaging in the striatum or nucleus accumbens requires nanosensors with an optimal dopamine dissociation constant (K) of 1 μM, whereas Ks above 10 μM are required for dopamine imaging in the prefrontal cortex. Furthermore, as a result of the probabilistic nature of dopamine terminal activity in the striatum, our model reveals that imaging frame rates of 20 Hz are optimal for recording temporally resolved dopamine release events. Our work provides a modeling platform to probe how complex neuromodulatory processes can be studied with fluorescent nanosensors and enables direct evaluation of nanosensor chemistry and imaging hardware parameters. Our stochastic model is generic for evaluating fluorescent neurotransmission probes, and is broadly applicable to the design of other neurotransmitter fluorophores and their optimization for implementation in vivo.

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    10/03/17 | Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex
    Homann J, Koay SA, Glidden AM, Tank DW, Berry MJ
    bioRxiv. 10/2017:. doi: 10.1101/197608

    To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

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    08/17/17 | Neurobiology: A bitter-sweet symphony.
    Li J, Luo L
    Nature. 08/2017;548(7667):285-287. doi: 10.1038/nature23537

    No abstract available.

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    08/15/17 | Dual near-Infrared two-photon microscopy for deep-tissue dopamine nanosensor imaging.
    Bonis-O'Donnell JT, Page RH, Beyene AG, Tindall EG, McFarlane IR, Landry MP
    Advanced Functional Materials. 2017 August 15;27(39):1702112. doi: 10.1002/adfm.v27.3910.1002/adfm.201702112

    A key limitation for achieving deep imaging in biological structures lies in photon absorption and scattering leading to attenuation of fluorescence. In particular, neurotransmitter imaging is challenging in the biologically relevant context of the intact brain for which photons must traverse the cranium, skin, and bone. Thus, fluorescence imaging is limited to the surface cortical layers of the brain, only achievable with craniotomy. Herein, this study describes optimal excitation and emission wavelengths for through‐cranium imaging, and demonstrates that near‐infrared emissive nanosensors can be photoexcited using a two‐photon 1560 nm excitation source. Dopamine‐sensitive nanosensors can undergo two‐photon excitation, and provide chirality‐dependent responses selective for dopamine with fluorescent turn‐on responses varying between 20% and 350%. The two‐photon absorption cross‐section and quantum yield of dopamine nanosensors are further calculated, and a two‐photon power law relationship for the nanosensor excitation process is confirmed. Finally, the improved image quality of the nanosensors embedded 2‐mm‐deep into a brain‐mimetic tissue phantom is shown, whereby one‐photon excitation yields 42% scattering, in contrast to 4% scattering when the same object is imaged under two‐photon excitation. The approach overcomes traditional limitations in deep‐tissue fluorescence microscopy, and can enable neurotransmitter imaging in the biologically relevant milieu of the intact and living brain.

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