Mass spectrometry and Monte Carlo method mapping of nanoparticle ligand shell morphology.

Abstract:

:Janus, patchy, stripe-like, or random arrangements of molecules within the ligand shell of nanoparticles affect many properties. Among all existing ligand shell morphology characterization methods, the one based on mass spectroscopy is arguably the simplest. Its greatest limitation is that the results are qualitative. Here, we use a tailor-made Monte Carlo type program that fits the whole MALDI spectrum and generates a 3D model of the ligand shell. Quantitative description of the ligand shell in terms of nearest neighbor distribution and characteristic length scale can be readily extracted by the model, and are compared with the results of other characterization methods. A parameter related to the intermolecular interaction is extracted when this method is combined with NMR. This approach could become the routine method to characterize the ligand shell morphology of many nanoparticles and we provide an open access program to facilitate its use.

journal_name

Nat Commun

journal_title

Nature communications

authors

Luo Z,Zhao Y,Darwish T,Wang Y,Hou J,Stellacci F

doi

10.1038/s41467-018-06939-y

subject

Has Abstract

pub_date

2018-10-26 00:00:00

pages

4478

issue

1

issn

2041-1723

pii

10.1038/s41467-018-06939-y

journal_volume

9

pub_type

杂志文章
  • Direct visualization of cell division using high-resolution imaging of M-phase of the cell cycle.

    abstract::Current approaches to monitor and quantify cell division in live cells, and reliably distinguish between acytokinesis and endoreduplication, are limited and complicate determination of stem cell pool identities. Here we overcome these limitations by generating an in vivo reporter system using the scaffolding protein a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2089

    authors: Hesse M,Raulf A,Pilz GA,Haberlandt C,Klein AM,Jabs R,Zaehres H,Fügemann CJ,Zimmermann K,Trebicka J,Welz A,Pfeifer A,Röll W,Kotlikoff MI,Steinhäuser C,Götz M,Schöler HR,Fleischmann BK

    更新日期:2012-01-01 00:00:00

  • Phototaxis of synthetic microswimmers in optical landscapes.

    abstract::Many microorganisms, with phytoplankton and zooplankton as prominent examples, display phototactic behaviour, that is, the ability to perform directed motion within a light gradient. Here we experimentally demonstrate that sensing of light gradients can also be achieved in a system of synthetic photo-activated micropa...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12828

    authors: Lozano C,Ten Hagen B,Löwen H,Bechinger C

    更新日期:2016-09-30 00:00:00

  • Broadband achromatic optical metasurface devices.

    abstract::Among various flat optical devices, metasurfaces have presented their great ability in efficient manipulation of light fields and have been proposed for variety of devices with specific functionalities. However, due to the high phase dispersion of their building blocks, metasurfaces significantly suffer from large chr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00166-7

    authors: Wang S,Wu PC,Su VC,Lai YC,Hung Chu C,Chen JW,Lu SH,Chen J,Xu B,Kuan CH,Li T,Zhu S,Tsai DP

    更新日期:2017-08-04 00:00:00

  • Water-induced correlation between single ions imaged at the solid-liquid interface.

    abstract::When immersed into water, most solids develop a surface charge, which is neutralized by an accumulation of dissolved counterions at the interface. Although the density distribution of counterions perpendicular to the interface obeys well-established theories, little is known about counterions' lateral organization at ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5400

    authors: Ricci M,Spijker P,Voïtchovsky K

    更新日期:2014-07-16 00:00:00

  • Electrically tunable optical polarization rotation on a silicon chip using Berry's phase.

    abstract::The continued convergence of electronics and photonics on the chip scale can benefit from the voltage control of optical polarization for applications in communications, signal processing and sensing. It is challenging, however, to electrically manipulate the polarization state of light in planar optical waveguides. H...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6337

    authors: Xu Q,Chen L,Wood MG,Sun P,Reano RM

    更新日期:2014-11-12 00:00:00

  • All-optical polariton transistor.

    abstract::Although optical technology provides the best solution for the transmission of information, all-optical devices must satisfy several qualitative criteria to be used as logic elements. In particular, cascadability is difficult to obtain in optical systems, and it is assured only if the output of one stage is in the cor...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2734

    authors: Ballarini D,De Giorgi M,Cancellieri E,Houdré R,Giacobino E,Cingolani R,Bramati A,Gigli G,Sanvitto D

    更新日期:2013-01-01 00:00:00

  • Active control of anapole states by structuring the phase-change alloy Ge2Sb2Te5.

    abstract::High-index dielectric nanoparticles supporting a distinct series of Mie resonances have enabled a new class of optical antennas with unprecedented functionalities. The great wealth of multipolar responses has not only brought in new physical insight but also spurred practical applications. However, how to make such a ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-08057-1

    authors: Tian J,Luo H,Yang Y,Ding F,Qu Y,Zhao D,Qiu M,Bozhevolnyi SI

    更新日期:2019-01-23 00:00:00

  • Microscopic origins of the terahertz carrier relaxation and cooling dynamics in graphene.

    abstract::The ultrafast dynamics of hot carriers in graphene are key to both understanding of fundamental carrier-carrier interactions and carrier-phonon relaxation processes in two-dimensional materials, and understanding of the physics underlying novel high-speed electronic and optoelectronic devices. Many recent experiments ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11617

    authors: Mihnev MT,Kadi F,Divin CJ,Winzer T,Lee S,Liu CH,Zhong Z,Berger C,de Heer WA,Malic E,Knorr A,Norris TB

    更新日期:2016-05-25 00:00:00

  • Studying an antiaromatic polycyclic hydrocarbon adsorbed on different surfaces.

    abstract::Antiaromatic and open-shell molecules are attractive because of their distinct electronic and magnetic behaviour. However, their increased reactivity creates a challenge for probing their properties. Here, we describe the on-surface and in-solution generation and characterisation of a highly reactive antiaromatic mole...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03368-9

    authors: Majzik Z,Pavliček N,Vilas-Varela M,Pérez D,Moll N,Guitián E,Meyer G,Peña D,Gross L

    更新日期:2018-03-22 00:00:00

  • GSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity.

    abstract::Iron (Fe) is essential for life, but in excess can cause oxidative cytotoxicity through the generation of Fe-catalyzed reactive oxygen species. It is yet unknown which genes and mechanisms can provide Fe-toxicity tolerance. Here, we identify S-nitrosoglutathione-reductase (GSNOR) variants underlying a major quantitati...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11892-5

    authors: Li B,Sun L,Huang J,Göschl C,Shi W,Chory J,Busch W

    更新日期:2019-08-29 00:00:00

  • Scaling law for excitons in 2D perovskite quantum wells.

    abstract::Ruddlesden-Popper halide perovskites are 2D solution-processed quantum wells with a general formula A2A'n-1M n X3n+1, where optoelectronic properties can be tuned by varying the perovskite layer thickness (n-value), and have recently emerged as efficient semiconductors with technologically relevant stability. However,...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04659-x

    authors: Blancon JC,Stier AV,Tsai H,Nie W,Stoumpos CC,Traoré B,Pedesseau L,Kepenekian M,Katsutani F,Noe GT,Kono J,Tretiak S,Crooker SA,Katan C,Kanatzidis MG,Crochet JJ,Even J,Mohite AD

    更新日期:2018-06-08 00:00:00

  • A cell-autonomous tumour suppressor role of RAF1 in hepatocarcinogenesis.

    abstract::Hepatocellular carcinoma (HCC) is a leading cause of cancer deaths, but its molecular heterogeneity hampers the design of targeted therapies. Currently, the only therapeutic option for advanced HCC is Sorafenib, an inhibitor whose targets include RAF. Unexpectedly, RAF1 expression is reduced in human HCC samples. Mode...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13781

    authors: Jeric I,Maurer G,Cavallo AL,Raguz J,Desideri E,Tarkowski B,Parrini M,Fischer I,Zatloukal K,Baccarini M

    更新日期:2016-12-21 00:00:00

  • Identification of the PGRMC1 protein complex as the putative sigma-2 receptor binding site.

    abstract::The sigma-2 receptor, whose gene remains to be cloned, has been validated as a biomarker for tumour cell proliferation. Here we report the use of a novel photoaffinity probe, WC-21, to identify the sigma-2 receptor-binding site. WC-21, a sigma-2 ligand containing both a photoactive azide moiety and a fluorescein isoth...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1386

    authors: Xu J,Zeng C,Chu W,Pan F,Rothfuss JM,Zhang F,Tu Z,Zhou D,Zeng D,Vangveravong S,Johnston F,Spitzer D,Chang KC,Hotchkiss RS,Hawkins WG,Wheeler KT,Mach RH

    更新日期:2011-07-05 00:00:00

  • High-throughput cell and spheroid mechanics in virtual fluidic channels.

    abstract::Microfluidics by soft lithography has proven to be of key importance for biophysics and life science research. While being based on replicating structures of a master mold using benchtop devices, design modifications are time consuming and require sophisticated cleanroom equipment. Here, we introduce virtual fluidic c...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15813-9

    authors: Panhwar MH,Czerwinski F,Dabbiru VAS,Komaragiri Y,Fregin B,Biedenweg D,Nestler P,Pires RH,Otto O

    更新日期:2020-05-04 00:00:00

  • Proximity-dependent initiation of hybridization chain reaction.

    abstract::Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8294

    authors: Koos B,Cane G,Grannas K,Löf L,Arngården L,Heldin J,Clausson CM,Klaesson A,Hirvonen MK,de Oliveira FM,Talibov VO,Pham NT,Auer M,Danielson UH,Haybaeck J,Kamali-Moghaddam M,Söderberg O

    更新日期:2015-06-12 00:00:00

  • MAP4K3 mediates amino acid-dependent regulation of autophagy via phosphorylation of TFEB.

    abstract::Autophagy is the major cellular pathway by which macromolecules are degraded, and amino acid depletion powerfully activates autophagy. MAP4K3, or germinal-center kinase-like kinase, is required for robust cell growth in response to amino acids, but the basis for MAP4K3 regulation of cellular metabolic disposition rema...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03340-7

    authors: Hsu CL,Lee EX,Gordon KL,Paz EA,Shen WC,Ohnishi K,Meisenhelder J,Hunter T,La Spada AR

    更新日期:2018-03-05 00:00:00

  • Actin-based confinement of calcium responses during Shigella invasion.

    abstract::Shigella, the agent of bacillary dysentery, invades epithelial cells by locally inducing actin reorganization. Upon cell invasion, Shigella induces calcium (Ca(2+)) signalling, but its role in invasion has remained unclear. Here we show that components involved in inositol 1, 4, 5- trisphosphate (InsP3) signalling are...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2561

    authors: Tran Van Nhieu G,Kai Liu B,Zhang J,Pierre F,Prigent S,Sansonetti P,Erneux C,Kuk Kim J,Suh PG,Dupont G,Combettes L

    更新日期:2013-01-01 00:00:00

  • Fetal-derived macrophages dominate in adult mammary glands.

    abstract::Macrophages serve multiple functions including immune regulation, morphogenesis, tissue homeostasis and healing reactions. The current paradigm holds that mammary gland macrophages first arise postnatally during the prepubertal period from the bone marrow-derived monocytes. Here we delineate the origins of tissue-resi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-08065-1

    authors: Jäppinen N,Félix I,Lokka E,Tyystjärvi S,Pynttäri A,Lahtela T,Gerke H,Elima K,Rantakari P,Salmi M

    更新日期:2019-01-17 00:00:00

  • Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.

    abstract::Lungs resected for adenocarcinomas often harbour minute discrete foci of cytologically atypical pneumocyte proliferations designated as atypical adenomatous hyperplasia (AAH). Evidence suggests that AAH represents an initial step in the progression to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MI...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9258

    authors: Izumchenko E,Chang X,Brait M,Fertig E,Kagohara LT,Bedi A,Marchionni L,Agrawal N,Ravi R,Jones S,Hoque MO,Westra WH,Sidransky D

    更新日期:2015-09-16 00:00:00

  • Inactivation of a CRF-dependent amygdalofugal pathway reverses addiction-like behaviors in alcohol-dependent rats.

    abstract::The activation of a neuronal ensemble in the central nucleus of the amygdala (CeA) during alcohol withdrawal has been hypothesized to induce high levels of alcohol drinking in dependent rats. In the present study we describe that the CeA neuronal ensemble that is activated by withdrawal from chronic alcohol exposure c...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09183-0

    authors: de Guglielmo G,Kallupi M,Pomrenze MB,Crawford E,Simpson S,Schweitzer P,Koob GF,Messing RO,George O

    更新日期:2019-03-18 00:00:00

  • Neural innervation stimulates splenic TFF2 to arrest myeloid cell expansion and cancer.

    abstract::CD11b(+)Gr-1(+) myeloid-derived suppressor cells (MDSCs) expand in the spleen during cancer and promote progression through suppression of cytotoxic T cells. An anti-inflammatory reflex arc involving the vagus nerve and memory T cells is necessary for resolution of acute inflammation. Failure of this neural circuit co...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10517

    authors: Dubeykovskaya Z,Si Y,Chen X,Worthley DL,Renz BW,Urbanska AM,Hayakawa Y,Xu T,Westphalen CB,Dubeykovskiy A,Chen D,Friedman RA,Asfaha S,Nagar K,Tailor Y,Muthupalani S,Fox JG,Kitajewski J,Wang TC

    更新日期:2016-02-04 00:00:00

  • Reciprocal regulation of the Il9 locus by counteracting activities of transcription factors IRF1 and IRF4.

    abstract::The T helper 9 (Th9) cell transcriptional network is formed by an equilibrium of signals induced by cytokines and antigen presentation. Here we show that, within this network, two interferon regulatory factors (IRF), IRF1 and IRF4, display opposing effects on Th9 differentiation. IRF4 dose-dependently promotes, wherea...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15366

    authors: Campos Carrascosa L,Klein M,Kitagawa Y,Lückel C,Marini F,König A,Guralnik A,Raifer H,Hagner-Benes S,Rädler D,Böck A,Kang C,Lohoff M,Garn H,Schaub B,Berberich-Siebelt F,Sakaguchi S,Bopp T,Huber M

    更新日期:2017-05-12 00:00:00

  • Mouse MRI shows brain areas relatively larger in males emerge before those larger in females.

    abstract::Sex differences exist in behaviors, disease and neuropsychiatric disorders. Sexual dimorphisms however, have yet to be studied across the whole brain and across a comprehensive time course of postnatal development. Here, we use manganese-enhanced MRI (MEMRI) to longitudinally image male and female C57BL/6J mice across...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04921-2

    authors: Qiu LR,Fernandes DJ,Szulc-Lerch KU,Dazai J,Nieman BJ,Turnbull DH,Foster JA,Palmert MR,Lerch JP

    更新日期:2018-07-05 00:00:00

  • Mutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food webs.

    abstract::Ecosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinator...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15688-w

    authors: Hale KRS,Valdovinos FS,Martinez ND

    更新日期:2020-05-01 00:00:00

  • DNA assembly for nanopore data storage readout.

    abstract::Synthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here,...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10978-4

    authors: Lopez R,Chen YJ,Dumas Ang S,Yekhanin S,Makarychev K,Racz MZ,Seelig G,Strauss K,Ceze L

    更新日期:2019-07-03 00:00:00

  • Human NK cell development requires CD56-mediated motility and formation of the developmental synapse.

    abstract::While distinct stages of natural killer (NK) cell development have been defined, the molecular interactions that shape human NK cell maturation are poorly understood. Here we define intercellular interactions between developing NK cells and stromal cells which, through contact-dependent mechanisms, promote the generat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12171

    authors: Mace EM,Gunesch JT,Dixon A,Orange JS

    更新日期:2016-07-20 00:00:00

  • Mapping ecologically relevant social behaviours by gene knockout in wild mice.

    abstract::The laboratory mouse serves as an important model system for studying gene, brain and behavioural interactions. Powerful methods of gene targeting have helped to decipher gene-function associations in human diseases. Yet, the laboratory mouse, obtained after decades of human-driven artificial selection, inbreeding, an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5569

    authors: Chalfin L,Dayan M,Levy DR,Austad SN,Miller RA,Iraqi FA,Dulac C,Kimchi T

    更新日期:2014-08-05 00:00:00

  • Tunable multiphase dynamics of arginine and lysine liquid condensates.

    abstract::Liquid phase separation into two or more coexisting phases has emerged as a new paradigm for understanding subcellular organization, prebiotic life, and the origins of disease. The design principles underlying biomolecular phase separation have the potential to drive the development of novel liquid-based organelles an...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18224-y

    authors: Fisher RS,Elbaum-Garfinkle S

    更新日期:2020-09-15 00:00:00

  • Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference.

    abstract::The heterogeneity of neurodegenerative diseases is a key confound to disease understanding and treatment development, as study cohorts typically include multiple phenotypes on distinct disease trajectories. Here we introduce a machine-learning technique-Subtype and Stage Inference (SuStaIn)-able to uncover data-driven...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05892-0

    authors: Young AL,Marinescu RV,Oxtoby NP,Bocchetta M,Yong K,Firth NC,Cash DM,Thomas DL,Dick KM,Cardoso J,van Swieten J,Borroni B,Galimberti D,Masellis M,Tartaglia MC,Rowe JB,Graff C,Tagliavini F,Frisoni GB,Laforce R Jr,Fin

    更新日期:2018-10-15 00:00:00

  • A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.

    abstract::Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12026

    authors: Arenz S,Bock LV,Graf M,Innis CA,Beckmann R,Grubmüller H,Vaiana AC,Wilson DN

    更新日期:2016-07-06 00:00:00