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Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data

Konarev, Petr V. ; Svergun, Dmitri I.

International Union of Crystallography (IUCr) ; 2018

In: IUCrJ Vol. 5, No. 4 ( 2018-07-01), p. 402-409

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In: IUCrJ, International Union of Crystallography (IUCr), Vol. 5, No. 4 ( 2018-07-01), p. 402-409

Abstract: Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro . Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.

Type of Medium: Online Resource

ISSN: 2052-2525

URL: Article

DOI: 10.1107/S2052252518005900

DOI: 10.1107/S2052252518005900/tj5014sup1.pdf

Language: Unknown

Publisher: International Union of Crystallography (IUCr)

Publication Date: 2018

detail.hit.zdb_id: 2754953-7

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Platinum Nanoparticles Generated in Functionality-Enhanced Reaction Media Based on Polyoctadecylsiloxane with Long-Chain Functional Modifiers

Shtykova, Eleonora V. ; Svergun, Dmitri I. ; Chernyshov, Dmitri M. ; [et al.]

American Chemical Society (ACS) ; 2004

In: The Journal of Physical Chemistry B Vol. 108, No. 20 ( 2004-05-01), p. 6175-6185

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In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 108, No. 20 ( 2004-05-01), p. 6175-6185

Type of Medium: Online Resource

ISSN: 1520-6106 , 1520-5207

URL: Article

DOI: 10.1021/jp049336b

RVK:

VA5430.B

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2004

detail.hit.zdb_id: 1357799-2

detail.hit.zdb_id: 2006039-7

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Formation of Metal Nanoparticles in Multilayered Poly(octadecylsiloxane) As Revealed by Anomalous Small-Angle X-ray Scattering

Svergun, Dmitri I. ; Kozin, Mikhail B. ; Konarev, Peter V. ; [et al.]

American Chemical Society (ACS) ; 2000

In: Chemistry of Materials Vol. 12, No. 12 ( 2000-12-01), p. 3552-3560

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In: Chemistry of Materials, American Chemical Society (ACS), Vol. 12, No. 12 ( 2000-12-01), p. 3552-3560

Type of Medium: Online Resource

ISSN: 0897-4756 , 1520-5002

URL: Article

DOI: 10.1021/cm001103j

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2000

detail.hit.zdb_id: 1500399-1

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Functional Polymer Colloids with Ordered Interior

Bronstein, Lyudmila M. ; Linton, Christina ; Karlinsey, Robert ; [et al.]

American Chemical Society (ACS) ; 2004

In: Langmuir Vol. 20, No. 4 ( 2004-02-01), p. 1100-1110

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In: Langmuir, American Chemical Society (ACS), Vol. 20, No. 4 ( 2004-02-01), p. 1100-1110

Type of Medium: Online Resource

ISSN: 0743-7463 , 1520-5827

URL: Article

DOI: 10.1021/la035951f

RVK:

VA 5760

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2004

detail.hit.zdb_id: 2005937-1

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Molecular model of a sensor of two-component signaling system

Ryzhykau, Yury L. ; Orekhov, Philipp S. ; Rulev, Maksim I. ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Scientific Reports Vol. 11, No. 1 ( 2021-05-24)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-05-24)

Abstract: Two-component systems (TCS) are widespread signaling systems present in all domains of life. TCS typically consist of a signal receptor/transducer and a response regulator. The receptors (histidine kinases, chemoreceptors and photoreceptors) are often embedded in the membrane and have a similar modular structure. Chemoreceptors were shown to function in highly ordered arrays, with trimers of dimers being the smallest functional unit. However, much less is known about photoreceptors. Here, we use small-angle scattering (SAS) to show that detergent-solubilized sensory rhodopsin II in complex with its cognate transducer forms dimers at low salt concentration, which associate into trimers of dimers at higher buffer molarities. We then fit an atomistic model of the whole complex into the SAS data. The obtained results suggest that the trimer of dimers is "tripod"-shaped and that the contacts between the dimers occur only through their cytoplasmic regions, whereas the transmembrane regions remain unconnected.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-021-89613-6

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2615211-3

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Metalated Diblock and Triblock Poly(ethylene oxide)-block-poly(4-vinylpyridine) Copolymers: Understanding of Micelle and Bulk Structure

Bronstein, Lyudmila M. ; Sidorov, Stanislav N. ; Zhirov, Vasilii ; [et al.]

American Chemical Society (ACS) ; 2005

In: The Journal of Physical Chemistry B Vol. 109, No. 40 ( 2005-10-01), p. 18786-18798

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In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 109, No. 40 ( 2005-10-01), p. 18786-18798

Type of Medium: Online Resource

ISSN: 1520-6106 , 1520-5207

URL: Article

DOI: 10.1021/jp053333x

DOI: 10.1021/jp053333x.s001

RVK:

VA5430.B

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2005

detail.hit.zdb_id: 1357799-2

detail.hit.zdb_id: 2006039-7

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Insights into complement convertase formation based on the structure of the factor B-cobra venom factor complex

Janssen, Bert J C ; Gomes, Lucio ; Koning, Roman I ; [et al.]

Wiley ; 2009

In: The EMBO Journal Vol. 28, No. 16 ( 2009-8-19), p. 2469-2478

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In: The EMBO Journal, Wiley, Vol. 28, No. 16 ( 2009-8-19), p. 2469-2478

Type of Medium: Online Resource

ISSN: 0261-4189 , 1460-2075

URL: Article

DOI: 10.1038/emboj.2009.184

RVK:

WA 15000

Language: Unknown

Publisher: Wiley

Publication Date: 2009

detail.hit.zdb_id: 1467419-1

detail.hit.zdb_id: 586044-1

SSG: 12

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X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism

Dadinova, Liubov A. ; Shtykova, Eleonora V. ; Konarev, Petr V. ; [et al.]

Public Library of Science (PLoS) ; 2016

In: PLOS ONE Vol. 11, No. 5 ( 2016-5-26), p. e0156105-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 5 ( 2016-5-26), p. e0156105-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0156105

DOI: 10.1371/journal.pone.0156105.g001

DOI: 10.1371/journal.pone.0156105.g002

DOI: 10.1371/journal.pone.0156105.g003

DOI: 10.1371/journal.pone.0156105.g004

DOI: 10.1371/journal.pone.0156105.g005

DOI: 10.1371/journal.pone.0156105.g006

DOI: 10.1371/journal.pone.0156105.g007

DOI: 10.1371/journal.pone.0156105.g008

DOI: 10.1371/journal.pone.0156105.t001

DOI: 10.1371/journal.pone.0156105.s001

DOI: 10.1371/journal.pone.0156105.s002

DOI: 10.1371/journal.pone.0156105.s003

DOI: 10.1371/journal.pone.0156105.s004

DOI: 10.1371/journal.pone.0156105.s005

DOI: 10.1371/journal.pone.0156105.s006

DOI: 10.1371/journal.pone.0156105.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2016

detail.hit.zdb_id: 2267670-3

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Block and Gradient Copoly(2-oxazoline) Micelles: Strikingly Different on the Inside

Filippov, Sergey K. ; Verbraeken, Bart ; Konarev, Petr V. ; [et al.]

American Chemical Society (ACS) ; 2017

In: The Journal of Physical Chemistry Letters Vol. 8, No. 16 ( 2017-08-17), p. 3800-3804

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In: The Journal of Physical Chemistry Letters, American Chemical Society (ACS), Vol. 8, No. 16 ( 2017-08-17), p. 3800-3804

Type of Medium: Online Resource

ISSN: 1948-7185 , 1948-7185

URL: Article

DOI: 10.1021/acs.jpclett.7b01588

DOI: 10.1021/acs.jpclett.7b01588.s001

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2017

detail.hit.zdb_id: 2522838-9

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The Crystal Structure of Netrin-1 in Complex with DCC Reveals the Bifunctionality of Netrin-1 As a Guidance Cue

Finci, Lorenzo I. ; Krüger, Nina ; Sun, Xiaqin ; [et al.]

Elsevier BV ; 2014

In: Neuron Vol. 83, No. 4 ( 2014-08), p. 839-849

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In: Neuron, Elsevier BV, Vol. 83, No. 4 ( 2014-08), p. 839-849

Type of Medium: Online Resource

ISSN: 0896-6273

URL: Article

DOI: 10.1016/j.neuron.2014.07.010

Language: English

Publisher: Elsevier BV

Publication Date: 2014

detail.hit.zdb_id: 2001944-0

SSG: 12

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