Conformational Dynamics of a Single Protein Monitored for 24 h at Video Rate

Ye, Weixiang; Götz, Markus; Celiksoy, Sirin; Tüting, Laura; Ratzke, Christoph; Prasad, Janak; Ricken, Julia; Wegner, Seraphine V.; Ahijado-Guzmán, Rubén; Hugel, Thorsten; Sönnichsen, Carsten

doi:10.1021/acs.nanolett.8b03342

Cited by 67 publications

(90 citation statements)

References 27 publications

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“…The optical dark-field spectroscopy setup used to record single-particle spectra was described in detail recently (36,44). Each nanoparticle receptor sensor has a characteristic plasmon resonance wavelength ( res ), which will have a spectral shift (⌬ res ) upon binding of biomolecules near the nanoparticle surface (37).…”

Section: Single-nanoparticle Plasmon Spectroscopy and Nanosprmentioning

confidence: 99%

Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein

Garg

Orru

et al. 2019

Journal of Biological Chemistry

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Edited by Joel M. Gottesfeld The mammalian CLOCK:BMAL1 transcription factor complex and its coactivators CREB-binding protein (CBP)/p300 and mixed-lineage leukemia 1 (MLL1) critically regulate circadian transcription and chromatin modification. Circadian oscillations are regulated by interactions of BMAL1's C-terminal transactivation domain (TAD) with the KIX domain of CBP/p300 (activating) and with the clock protein CRY1 (repressing) as well as by the BMAL1 G-region preceding the TAD. Circadian acetylation of Lys 537 within the G-region enhances repressive BMAL1-TAD-CRY1 interactions. Here, we characterized the interaction of the CBP-KIX domain with BMAL1 proteins, including the BMAL1-TAD, parts of the G-region, and Lys 537. Tethering the small compound 1-10 in the MLL-binding pocket of the CBP-KIX domain weakened BMAL1 binding, and MLL1-bound KIX did not form a ternary complex with BMAL1, indicating that the MLL-binding pocket is important for KIX-BMAL1 interactions. Small-angle X-ray scattering (SAXS) models of BMAL1 and BMAL1:KIX complexes revealed that the N-terminal BMAL1 G-region including Lys 537 forms elongated extensions emerging from the bulkier BMAL1-TAD:KIX core complex. Fitting high-resolution KIX domain structures into the SAXS-derived envelopes suggested that the G-region emerges near the MLL-binding pocket, further supporting a role of this pocket in BMAL1 binding. Additionally, mutations in the second CREB-pKID/c-Myb-binding pocket of the KIX domain moderately impacted BMAL1 binding. The BMAL1(K537Q) mutation mimicking Lys 537 acetylation, however, did not affect the KIX-binding affinity, in contrast to its enhancing effect on CRY1 binding. Our results significantly advance the mechanistic understanding of the protein interaction networks controlling CLOCK:BMAL1-and CBP-dependent gene regulation in the mammalian circadian clock. Most organisms possess circadian rhythms coordinated by circadian clocks that synchronize them to the 24-h light-dark cycle. In mammals, circadian rhythmicity is controlled by transcriptional/translational feedback loops. The core transcriptional/translational feedback loop consists of the heterodimeric basic helix-loop-helix (bHLH) 4-PER-ARNT-SIM (PAS) domaincontaining transcriptional activators CLOCK (circadian locomotor output cycle kaput) and BMAL1 (brain and muscle ARNT-like protein-1), which circadianly regulate genes encoding Period (PER1, PER2, and PER3) and Cryptochrome (CRY1 and CRY2) clock proteins as well as many clock-controlled genes (1, 2). Analyses in mouse liver led to a model of three temporally separated states of CLOCK:BMAL1-dependent circadian transcription: an early repressive state, a late repressive state, and an active state (3). Large multisubunit PER-and CRY-containing complexes interact with CLOCK:BMAL1 in the early phase of repression (4), whereas CRY1 alone maintains the late repressive state (5, 6). In the active state, CLOCK:BMAL1 associates with co-activators such as the histone acetyl transferase CREB-binding protein (CBP) and its paralo...

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Section: Single-nanoparticle Plasmon Spectroscopy and Nanosprmentioning

confidence: 99%

Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein

Garg

Orru

et al. 2019

Journal of Biological Chemistry

Self Cite

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“…The current generation of metal-oxide semiconductor (sCMOS) detectors enables simultaneous imaging of 1 x 10 4 molecules in a total internal fluorescence microscopy (TIRFM) configuration and can be coupled with nanofabricated zeromode waveguides (ZMWs) to enable access to high concentrations [5][6][7] . Non-fluorescence-based single-molecule experiments such as plasmon rulers, scattering, magnetic tweezers, and singlemolecule centrifugation generate a tremendous amount of data through parallel measurement of hundreds of molecules with orders of magnitude longer recordings than a typical fluorescence experiment [8][9][10][11][12] .…”

Section: Introductionmentioning

confidence: 99%

Top-down machine learning approach for high-throughput single-molecule analysis

White

Goldschen-Ohm

Goldsmith

et al. 2020

eLife

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Single-molecule approaches provide enormous insight into the dynamics of biomolecules, but adequately sampling distributions of states and events often requires extensive sampling. Although emerging experimental techniques can generate such large datasets, existing analysis tools are not suitable to process the large volume of data obtained in high-throughput paradigms. Here, we present a new analysis platform (DISC) that accelerates unsupervised analysis of single-molecule trajectories. By merging model-free statistical learning with the Viterbi algorithm, DISC idealizes single-molecule trajectories up to three orders of magnitude faster with improved accuracy compared to other commonly used algorithms. Further, we demonstrate the utility of DISC algorithm to probe cooperativity between multiple binding events in the cyclic nucleotide binding domains of HCN pacemaker channel. Given the flexible and efficient nature of DISC, we anticipate it will be a powerful tool for unsupervised processing of high-throughput data across a range of single-molecule experiments.

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“…Localized surface plasmon resonance (LSPR) of metal nanoparticles induced by incident light has gained considerable attention because of its great potential for a wide range of applications in areas such as catalysis, photonics, electronics, and biomedicine . In solar energy conversion, metal nanoparticles exhibit good potential to effectively enhance the light harvesting efficiency of devices by extending and increasing light absorption or scattering introduced by LSPR, which depend on the size, morphology, and composition of metal nanoparticles .…”

Section: Introductionmentioning

confidence: 99%

Growing In‐Plane Multiplex Plasmonic Arrays for Synergistic Enhanced Photocurrent Response

Liang

Sun

et al. 2019

Adv Materials Inter

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A complete control of the localized surface plasmon resonance (LSPR) properties of different types of metal nanoparticles (size, shape, or composition) in a device by facile techniques with high throughput is crucial to intensively study and apply the LSPR effects to improve device performance. Here, a versatile approach is presented to fabricate macroscopic and in‐plane multiplex arrays of plasmonic nanoparticles with well‐defined particle size or composition allocation. The polymer layer (poly(N‐isopropylacrylamide), PNIPAM) spin‐coated on the surface of the substrate is applied as a protective layer to control the growth of the Au nanoparticles in a dip‐coating procedure. The relative contribution of LSPR of each particle type can be controlled by selectively adjusting the particle size or composition at the desired position of multiplex arrays on the same substrate. A synergistic enhanced photocurrent response is observed in the metal–semiconductor system, which is attributed to broadened LSPR enhancement of multiplex composition (Au and Au@Ag) structures from the same substrate. The fabrication procedure presented in this study is highly repeatable and feasible for preparing ordered multiplex nanostructures on the same substrate. Furthermore, this method provides a cost‐effective and versatile platform for design of multiplex plasmonic nanostructures in sensing, solar energy conversion, and optical processing applications.

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Conformational Dynamics of a Single Protein Monitored for 24 h at Video Rate

Cited by 67 publications

References 27 publications

Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein

Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein

Top-down machine learning approach for high-throughput single-molecule analysis

Growing In‐Plane Multiplex Plasmonic Arrays for Synergistic Enhanced Photocurrent Response

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