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1.
Nat Methods ; 18(10): 1247-1252, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34608319

RESUMO

The quantification of membrane-associated biomolecular interactions is crucial to our understanding of various cellular processes. State-of-the-art single-molecule approaches rely largely on the addition of fluorescent labels, which complicates the quantification of the involved stoichiometries and dynamics because of low temporal resolution and the inherent limitations associated with labeling efficiency, photoblinking and photobleaching. Here, we demonstrate dynamic mass photometry, a method for label-free imaging, tracking and mass measurement of individual membrane-associated proteins diffusing on supported lipid bilayers. Application of this method to the membrane remodeling GTPase, dynamin-1, reveals heterogeneous mixtures of dimer-based oligomers, oligomer-dependent mobilities, membrane affinities and (dis)association of individual complexes. These capabilities, together with assay-based advances for studying integral membrane proteins, will enable the elucidation of biomolecular mechanisms in and on lipid bilayers.

2.
Nanoscale ; 13(29): 12687-12696, 2021 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-34477619

RESUMO

Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable statistics. Here, we present a molecular force sensor and charge detector based on parallelised imaging and tracking of tethered double-stranded DNA functionalised with charged nanoparticles interacting with an externally applied electric field. Tracking the position of the tethered particle with simultaneous nanometre precision and microsecond temporal resolution allows us to detect and quantify the electrophoretic force down to the sub-piconewton scale. Furthermore, we demonstrate that this approach is suitable for detecting changes to the particle charge state, as induced by the addition of charged biomolecules or changes to pH. Our approach provides an alternative route to studying structural and charge dynamics at the single molecule level.


Assuntos
Nanopartículas , Nanotecnologia , DNA , Eletroforese
3.
Structure ; 2021 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-34492227

RESUMO

R2TP is a highly conserved chaperone complex formed by two AAA+ ATPases, RUVBL1 and RUVBL2, that associate with PIH1D1 and RPAP3 proteins. R2TP acts in promoting macromolecular complex formation. Here, we establish the principles of R2TP assembly. Three distinct RUVBL1/2-based complexes are identified: R2TP, RUVBL1/2-RPAP3 (R2T), and RUVBL1/2-PIH1D1 (R2P). Interestingly, we find that PIH1D1 does not bind to RUVBL1/RUVBL2 in R2TP and does not function as a nucleotide exchange factor; instead, RPAP3 is found to be the central subunit coordinating R2TP architecture and linking PIH1D1 and RUVBL1/2. We also report that RPAP3 contains an intrinsically disordered N-terminal domain mediating interactions with substrates whose sequences are primarily enriched for Armadillo repeat domains and other helical-type domains. Our work provides a clear and consistent model of R2TP complex structure and gives important insights into how a chaperone machine concerned with assembly of folded proteins into multisubunit complexes might work.

4.
Chem Rev ; 121(19): 11937-11970, 2021 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-34587448

RESUMO

Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.

5.
Phys Chem Chem Phys ; 23(31): 16488-16500, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34342317

RESUMO

Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.


Assuntos
Proteínas/química , Cinética , Fenômenos Ópticos , Ligação Proteica , Proteínas/metabolismo
6.
Elife ; 102021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34328418

RESUMO

In Gram-positive bacteria, the McsB protein arginine kinase is central to protein quality control, labeling aberrant molecules for degradation by the ClpCP protease. Despite its importance for stress response and pathogenicity, it is still elusive how the bacterial degradation labeling is regulated. Here, we delineate the mechanism how McsB targets aberrant proteins during stress conditions. Structural data reveal a self-compartmentalized kinase, in which the active sites are sequestered in a molecular cage. The 'closed' octamer interconverts with other oligomers in a phosphorylation-dependent manner and, unlike these 'open' forms, preferentially labels unfolded proteins. In vivo data show that heat-shock triggers accumulation of higher order oligomers, of which the octameric McsB is essential for surviving stress situations. The interconversion of open and closed oligomers represents a distinct regulatory mechanism of a degradation labeler, allowing the McsB kinase to adapt its potentially dangerous enzyme function to the needs of the bacterial cell.


Assuntos
Bacillus subtilis/genética , Proteínas de Bactérias/metabolismo , Proteínas Quinases/genética , Proteínas Quinases/metabolismo , Bacillus subtilis/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Fosforilação , Proteínas Quinases/química
7.
Elife ; 102021 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-34142657

RESUMO

The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase for linear/Met1-linked ubiquitin chain formation. One of the LUBAC components, heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L), was recently shown to catalyse oxyester bond formation between ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. Here, we present the first 3D reconstruction of human LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that this event depends on HOIL-1L catalytic activity. By cross-linking mass spectrometry showing proximity between the catalytic RING-in-between-RING (RBR) domains, a coordinated ubiquitin relay mechanism between the HOIL-1-interacting protein (HOIP) and HOIL-1L ligases is suggested. In mouse embryonic fibroblasts, these heterotypic chains were induced by TNF, which is reduced in cells expressing an HOIL-1L catalytic inactive mutant. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains by the concerted action of HOIP and HOIL-1L.

8.
J Mol Biol ; 432(23): 6168-6172, 2020 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-33068635

RESUMO

The αß-tubulin heterodimer is the fundamental building block of microtubules, making it central to several cellular processes. Despite the apparent simplicity of heterodimerisation, the associated energetics and kinetics remain disputed, largely due to experimental challenges associated with quantifying affinities in the <µM range. We use mass photometry to observe tubulin monomers and heterodimers in solution simultaneously, thereby quantifying the αß-tubulin dissociation constant (8.48 ± 1.22 nM) and its tightening in the presence of GTP (3.69 ± 0.65 nM), at a dissociation rate >10-2 s-1. Our results demonstrate the capabilities of mass photometry for quantifying protein-protein interactions and clarify the energetics and kinetics of tubulin heterodimerisation.


Assuntos
Conformação Proteica , Mapas de Interação de Proteínas/genética , Tubulina (Proteína)/genética , Animais , Guanosina Trifosfato/metabolismo , Cinética , Fotometria , Multimerização Proteica/genética , Termodinâmica , Tubulina (Proteína)/química
9.
Nucleic Acids Res ; 48(17): e97, 2020 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-32756898

RESUMO

Mass photometry is a recently developed methodology capable of measuring the mass of individual proteins under solution conditions. Here, we show that this approach is equally applicable to nucleic acids, enabling their facile, rapid and accurate detection and quantification using sub-picomoles of sample. The ability to count individual molecules directly measures relative concentrations in complex mixtures without need for separation. Using a dsDNA ladder, we find a linear relationship between the number of bases per molecule and the associated imaging contrast for up to 1200 bp, enabling us to quantify dsDNA length with up to 2 bp accuracy. These results introduce mass photometry as an accurate, rapid and label-free single molecule method complementary to existing DNA characterization techniques.


Assuntos
DNA/química , Espectrometria de Massas/métodos , Fotometria/métodos , Imagem Individual de Molécula/métodos , DNA/análise
10.
ACS Nano ; 14(9): 11160-11168, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32790332

RESUMO

Studying dynamic self-assembling systems in their native environment is essential for understanding the mechanisms of self-assembly and thereby exerting full control over these processes. Traditional ensemble-based analysis methods often struggle to reveal critical features of the self-assembly that occur at the single particle level. Here, we describe a label-free single-particle assay to visualize real-time self-assembly in aqueous solutions by interferometric scattering microscopy. We demonstrate how the assay can be applied to biphasic reactions yielding micellar or vesicular aggregates, detecting the onset of aggregate formation, quantifying the kinetics at the single particle level, and distinguishing sigmoidal and exponential growth of aggregate populations. Furthermore, we can follow the evolution in aggregate size in real time, visualizing the nucleation stages of the self-assembly processes and record phenomena such as incorporation of oily components into the micelle or vesicle lumen.


Assuntos
Interferometria , Microscopia , Cinética , Micelas , Água
11.
Angew Chem Int Ed Engl ; 59(46): 20361-20366, 2020 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-32706135

RESUMO

We report chemically fuelled out-of-equilibrium self-replicating vesicles based on surfactant formation. We studied the vesicles' autocatalytic formation using UPLC to determine monomer concentration and interferometric scattering microscopy at the nanoparticle level. Unlike related reports of chemically fuelled self-replicating micelles, our vesicular system was too stable to surfactant degradation to be maintained out of equilibrium. The introduction of a catalyst, which introduces a second catalytic cycle into the metabolic network, was used to close the first cycle. This shows how coupled catalytic cycles can create a metabolic network that allows the creation and perseverance of fuel-driven, out-of-equilibrium self-replicating vesicles.

12.
Nat Commun ; 11(1): 1772, 2020 04 14.
Artigo em Inglês | MEDLINE | ID: mdl-32286308

RESUMO

Sample purity is central to in vitro studies of protein function and regulation, and to the efficiency and success of structural studies using techniques such as x-ray crystallography and cryo-electron microscopy (cryo-EM). Here, we show that mass photometry (MP) can accurately characterize the heterogeneity of a sample using minimal material with high resolution within a matter of minutes. To benchmark our approach, we use negative stain electron microscopy (nsEM), a popular method for EM sample screening. We include typical workflows developed for structure determination that involve multi-step purification of a multi-subunit ubiquitin ligase and chemical cross-linking steps. When assessing the integrity and stability of large molecular complexes such as the proteasome, we detect and quantify assemblies invisible to nsEM. Our results illustrate the unique advantages of MP over current methods for rapid sample characterization, prioritization and workflow optimization.


Assuntos
Microscopia Crioeletrônica/métodos , Espectrometria de Massas/métodos , Ciclossomo-Complexo Promotor de Anáfase/metabolismo , Animais , Bovinos , Eletroforese em Gel de Poliacrilamida , Escherichia coli/genética , Escherichia coli/ultraestrutura , Complexo de Endopeptidases do Proteassoma/metabolismo , Ligação Proteica
13.
Biophys J ; 118(8): 1946-1957, 2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32191863

RESUMO

The plasma membrane and the underlying cytoskeletal cortex constitute active platforms for a variety of cellular processes. Recent work has shown that the remodeling acto-myosin network modifies local membrane organization, but the molecular details are only partly understood because of difficulties with experimentally accessing the relevant time and length scales. Here, we use interferometric scattering microscopy to investigate a minimal acto-myosin network linked to a supported lipid bilayer membrane. Using the magnitude of the interferometric contrast, which is proportional to molecular mass, and fast acquisition rates, we detect and image individual membrane-attached actin filaments diffusing within the acto-myosin network and follow individual myosin II filament dynamics. We quantify myosin II filament dwell times and processivity as functions of ATP concentration, providing experimental evidence for the predicted ensemble behavior of myosin head domains. Our results show how decreasing ATP concentrations lead to both increasing dwell times of individual myosin II filaments and a global change from a remodeling to a contractile state of the acto-myosin network.


Assuntos
Actinas , Microscopia , Citoesqueleto de Actina , Miosina Tipo II , Miosinas
14.
J Phys Chem A ; 124(13): 2721-2730, 2020 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-32130861

RESUMO

We present a statistical analysis of femtosecond transient absorption microscopy applied to four different organic semiconductor thin films based on perylene-diimide (PDI). By achieving a temporal resolution of 12 fs with simultaneous sub-10 nm spatial precision, we directly probe the underlying exciton transport characteristics within 3 ps after photoexcitation free of model assumptions. Our study reveals sub-picosecond coherent exciton transport (12-45 cm2 s-1) followed by a diffusive phase of exciton transport (3-17 cm2 s-1). A comparison between the different films suggests that the exciton transport in the studied materials is intricately linked to their nanoscale morphology, with PDI films that form large crystalline domains exhibiting the largest diffusion coefficients and transport lengths. Our study demonstrates the advantages of directly studying ultrafast transport properties at the nanometer length scale and highlights the need to examine nanoscale morphology when investigating exciton transport in organic as well as inorganic semiconductors.

15.
Angew Chem Int Ed Engl ; 59(27): 10774-10779, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32167227

RESUMO

Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.


Assuntos
Proteínas/química , Espectrofotometria Ultravioleta/métodos , Cinética
16.
J Phys Chem Lett ; 10(21): 6727-6733, 2019 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-31592672

RESUMO

We present a novel optical transient absorption and reflection microscope based on a diffraction-limited pump pulse in combination with a wide-field probe pulse, for the spatiotemporal investigation of ultrafast population transport in thin films. The microscope achieves a temporal resolution down to 12 fs and simultaneously provides sub-10 nm spatial accuracy. We demonstrate the capabilities of the microscope by revealing an ultrafast excited-state exciton population transport of up to 32 nm in a thin film of pentacene and by tracking the carrier motion in p-doped silicon. The use of few-cycle optical excitation pulses enables impulsive stimulated Raman microspectroscopy, which is used for in situ verification of the chemical identity in the 100-2000 cm-1 spectral window. Our methodology bridges the gap between optical microscopy and spectroscopy, allowing for the study of ultrafast transport properties down to the nanometer length scale.

18.
Nat Commun ; 10(1): 4207, 2019 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-31527736

RESUMO

The complex dynamics of ultrafast photoinduced reactions are governed by their evolution along vibronically coupled potential energy surfaces. It is now often possible to identify such processes, but a detailed depiction of the crucial nuclear degrees of freedom involved typically remains elusive. Here, combining excited-state time-domain Raman spectroscopy and tree-tensor network state simulations, we construct the full 108-atom molecular movie of ultrafast singlet fission in a pentacene dimer, explicitly treating 252 vibrational modes on 5 electronic states. We assign the tuning and coupling modes, quantifying their relative intensities and contributions, and demonstrate how these modes coherently synchronise to drive the reaction. Our combined experimental and theoretical approach reveals the atomic-scale singlet fission mechanism and can be generalized to other ultrafast photoinduced reactions in complex systems. This will enable mechanistic insight on a detailed structural level, with the ultimate aim to rationally design molecules to maximise the efficiency of photoinduced reactions.

20.
Nature ; 569(7756): 438-442, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31068697

RESUMO

Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery1, and have inspired synthetic biologists to create novel protein assemblies via the precise manipulation of protein-protein interfaces. Despite the impressive array of protein cages produced in the laboratory, the design of inducible assemblies remains challenging2,3. Here we demonstrate an ultra-stable artificial protein cage, the assembly and disassembly of which can be controlled by metal coordination at the protein-protein interfaces. The addition of a gold (I)-triphenylphosphine compound to a cysteine-substituted, 11-mer protein ring triggers supramolecular self-assembly, which generates monodisperse cage structures with masses greater than 2 MDa. The geometry of these structures is based on the Archimedean snub cube and is, to our knowledge, unprecedented. Cryo-electron microscopy confirms that the assemblies are held together by 120 S-Aui-S staples between the protein oligomers, and exist in two chiral forms. The cage shows extreme chemical and thermal stability, yet it readily disassembles upon exposure to reducing agents. As well as gold, mercury(II) is also found to enable formation of the protein cage. This work establishes an approach for linking protein components into robust, higher-order structures, and expands the design space available for supramolecular assemblies to include previously unexplored geometries.


Assuntos
Ouro/química , Proteínas/química , Microscopia Crioeletrônica , Cisteína/química , Mercúrio/química , Modelos Moleculares , Proteínas/ultraestrutura
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