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A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

Zhao, Huaying ; Ghirlando, Rodolfo ; Alfonso, Carlos ; [et al.]

Public Library of Science (PLoS) ; 2015

In: PLOS ONE Vol. 10, No. 5 ( 2015-5-21), p. e0126420-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 10, No. 5 ( 2015-5-21), p. e0126420-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0126420

DOI: 10.1371/journal.pone.0126420.g001

DOI: 10.1371/journal.pone.0126420.g002

DOI: 10.1371/journal.pone.0126420.g003

DOI: 10.1371/journal.pone.0126420.g004

DOI: 10.1371/journal.pone.0126420.g005

DOI: 10.1371/journal.pone.0126420.g006

DOI: 10.1371/journal.pone.0126420.g007

DOI: 10.1371/journal.pone.0126420.g008

DOI: 10.1371/journal.pone.0126420.g009

DOI: 10.1371/journal.pone.0126420.g010

DOI: 10.1371/journal.pone.0126420.g011

DOI: 10.1371/journal.pone.0126420.g012

DOI: 10.1371/journal.pone.0126420.g013

DOI: 10.1371/journal.pone.0126420.g014

DOI: 10.1371/journal.pone.0126420.s001

DOI: 10.1371/journal.pone.0126420.s002

DOI: 10.1371/journal.pone.0126420.s003

DOI: 10.1371/journal.pone.0126420.s004

DOI: 10.1371/journal.pone.0126420.s005

DOI: 10.1371/journal.pone.0126420.s006

DOI: 10.1371/journal.pone.0126420.s007

DOI: 10.1371/journal.pone.0126420.s008

DOI: 10.1371/journal.pone.0126420.s009

DOI: 10.1371/journal.pone.0126420.s010

DOI: 10.1371/journal.pone.0126420.s011

DOI: 10.1371/journal.pone.0126420.s012

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2015

detail.hit.zdb_id: 2267670-3

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Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study

López-Méndez, Blanca ; Baron, Bruno ; Brautigam, Chad A. ; [et al.]

Springer Science and Business Media LLC ; 2021

In: European Biophysics Journal Vol. 50, No. 3-4 ( 2021-05), p. 411-427

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In: European Biophysics Journal, Springer Science and Business Media LLC, Vol. 50, No. 3-4 ( 2021-05), p. 411-427

Abstract: Microscale thermophoresis (MST), and the closely related Temperature Related Intensity Change (TRIC), are synonyms for a recently developed measurement technique in the field of biophysics to quantify biomolecular interactions, using the (capillary-based) NanoTemper Monolith and (multiwell plate-based) Dianthus instruments. Although this technique has been extensively used within the scientific community due to its low sample consumption, ease of use, and ubiquitous applicability, MST/TRIC has not enjoyed the unambiguous acceptance from biophysicists afforded to other biophysical techniques like isothermal titration calorimetry (ITC) or surface plasmon resonance (SPR). This might be attributed to several facts, e.g., that various (not fully understood) effects are contributing to the signal, that the technique is licensed to only a single instrument developer, NanoTemper Technology, and that its reliability and reproducibility have never been tested independently and systematically. Thus, a working group of ARBRE-MOBIEU has set up a benchmark study on MST/TRIC to assess this technique as a method to characterize biomolecular interactions. Here we present the results of this study involving 32 scientific groups within Europe and two groups from the US, carrying out experiments on 40 Monolith instruments , employing a standard operation procedure and centrally prepared samples. A protein–small molecule interaction, a newly developed protein–protein interaction system and a pure dye were used as test systems. We characterized the instrument properties and evaluated instrument performance, reproducibility, the effect of different analysis tools, the influence of the experimenter during data analysis, and thus the overall reliability of this method.

Type of Medium: Online Resource

ISSN: 0175-7571 , 1432-1017

URL: Article

DOI: 10.1007/s00249-021-01532-6

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 1398349-0

SSG: 12

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Structures of Normal Single-Stranded DNA and Deoxyribo-3‘- S -phosphorothiolates Bound to the 3‘-5‘ Exonucleolytic Active Site of DNA Polymerase I from Escherichia coli ,

Brautigam, Chad A. ; Sun, Sengen ; Piccirilli, Joseph A. ; [et al.]

American Chemical Society (ACS) ; 1999

In: Biochemistry Vol. 38, No. 2 ( 1999-01-01), p. 696-704

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In: Biochemistry, American Chemical Society (ACS), Vol. 38, No. 2 ( 1999-01-01), p. 696-704

Type of Medium: Online Resource

ISSN: 0006-2960 , 1520-4995

URL: Article

DOI: 10.1021/bi981537g

RVK:

WA 15000

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 1999

detail.hit.zdb_id: 1472258-6

SSG: 12

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Correction to: Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study

López-Méndez, Blanca ; Baron, Bruno ; Brautigam, Chad A. ; [et al.]

Springer Science and Business Media LLC ; 2021

In: European Biophysics Journal Vol. 50, No. 8 ( 2021-12), p. 1159-1160

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In: European Biophysics Journal, Springer Science and Business Media LLC, Vol. 50, No. 8 ( 2021-12), p. 1159-1160

Type of Medium: Online Resource

ISSN: 0175-7571 , 1432-1017

URL: Article

DOI: 10.1007/s00249-021-01573-x

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 1398349-0

SSG: 12

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Structural basis of arrestin-3 activation and signaling

Chen, Qiuyan ; Perry, Nicole A. ; Vishnivetskiy, Sergey A. ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Nature Communications Vol. 8, No. 1 ( 2017-11-10)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2017-11-10)

Abstract: A unique aspect of arrestin-3 is its ability to support both receptor-dependent and receptor-independent signaling. Here, we show that inositol hexakisphosphate (IP 6 ) is a non-receptor activator of arrestin-3 and report the structure of IP 6 -activated arrestin-3 at 2.4-Å resolution. IP 6 -activated arrestin-3 exhibits an inter-domain twist and a displaced C-tail, hallmarks of active arrestin. IP 6 binds to the arrestin phosphate sensor, and is stabilized by trimerization. Analysis of the trimerization surface, which is also the receptor-binding surface, suggests a feature called the finger loop as a key region of the activation sensor. We show that finger loop helicity and flexibility may underlie coupling to hundreds of diverse receptors and also promote arrestin-3 activation by IP 6 . Importantly, we show that effector-binding sites on arrestins have distinct conformations in the basal and activated states, acting as switch regions. These switch regions may work with the inter-domain twist to initiate and direct arrestin-mediated signaling.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-017-01218-8

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2553671-0

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The Haemophilus ducreyi Fis Protein Is Involved in Controlling Expression of the lspB-lspA2 Operon and Other Virulence Factors

Labandeira-Rey, Maria ; Dodd, Dana A. ; Brautigam, Chad A. ; [et al.]

American Society for Microbiology ; 2013

In: Infection and Immunity Vol. 81, No. 11 ( 2013-11), p. 4160-4170

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In: Infection and Immunity, American Society for Microbiology, Vol. 81, No. 11 ( 2013-11), p. 4160-4170

Abstract: Expression of the lspB-lspA2 operon encoding a virulence-related two-partner secretion system in Haemophilus ducreyi 35000HP is directly regulated by the CpxRA regulatory system (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402–3411, 2009). In the present study, we show that this secretion system is also regulated by the small nucleoid-associated protein Fis. Inactivation of the H. ducreyi fis gene resulted in a reduction in expression of both the H. ducreyi LspB and LspA2 proteins. DNA microarray experiments showed that a H. ducreyi fis deletion mutant exhibited altered expression levels of genes encoding other important H. ducreyi virulence factors, including DsrA and Flp1, suggesting a possible global role for Fis in the control of virulence in this obligate human pathogen. While the H. ducreyi Fis protein has a high degree of sequence and structural similarity to the Fis proteins of other bacteria, its temporal pattern of expression was very different from that of enterobacterial Fis proteins. The use of a lacZ -based transcriptional reporter provided evidence which indicated that the H. ducreyi Fis homolog is a positive regulator of gyrB , a gene that is negatively regulated by Fis in enteric bacteria. Taken together, the Fis protein expression data and the observed regulatory effects of Fis in H. ducreyi suggest that this small DNA binding protein has a regulatory role in H. ducreyi which may differ in substantial ways from that of other Fis proteins.

Type of Medium: Online Resource

ISSN: 0019-9567 , 1098-5522

URL: Article

DOI: 10.1128/IAI.00714-13

RVK:

XA 10000

Language: English

Publisher: American Society for Microbiology

Publication Date: 2013

detail.hit.zdb_id: 1483247-1

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Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates

Brautigam, Chad A ; Steitz, Thomas A

Elsevier BV ; 1998

In: Journal of Molecular Biology Vol. 277, No. 2 ( 1998-03), p. 363-377

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In: Journal of Molecular Biology, Elsevier BV, Vol. 277, No. 2 ( 1998-03), p. 363-377

Type of Medium: Online Resource

ISSN: 0022-2836

URL: Article

DOI: 10.1006/jmbi.1997.1586

Language: English

Publisher: Elsevier BV

Publication Date: 1998

detail.hit.zdb_id: 1355192-9

SSG: 12

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Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes

Brautigam, Chad A ; Steitz, Thomas A

Elsevier BV ; 1998

In: Current Opinion in Structural Biology Vol. 8, No. 1 ( 1998-02), p. 54-63

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In: Current Opinion in Structural Biology, Elsevier BV, Vol. 8, No. 1 ( 1998-02), p. 54-63

Type of Medium: Online Resource

ISSN: 0959-440X

URL: Article

DOI: 10.1016/S0959-440X(98)80010-9

Language: English

Publisher: Elsevier BV

Publication Date: 1998

detail.hit.zdb_id: 2019233-2

SSG: 12

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The Cdc20-binding Phe Box of the Spindle Checkpoint Protein BubR1 Maintains the Mitotic Checkpoint Complex During Mitosis

Diaz-Martinez, Laura A. ; Tian, Wei ; Li, Bing ; [et al.]

Elsevier BV ; 2015

In: Journal of Biological Chemistry Vol. 290, No. 4 ( 2015-01), p. 2431-2443

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In: Journal of Biological Chemistry, Elsevier BV, Vol. 290, No. 4 ( 2015-01), p. 2431-2443

Type of Medium: Online Resource

ISSN: 0021-9258

URL: Article

DOI: 10.1074/jbc.M114.616490

Language: English

Publisher: Elsevier BV

Publication Date: 2015

detail.hit.zdb_id: 2141744-1

detail.hit.zdb_id: 1474604-9

SSG: 12

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Ayaz, Pelin ; Munyoki, Sarah ; Geyer, Elisabeth A ; [et al.]

eLife Sciences Publications, Ltd ; 2014

In: eLife Vol. 3 ( 2014-08-05)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 3 ( 2014-08-05)

Abstract: Dynamic filaments of proteins, called microtubules, have several important roles inside cells. Microtubules provide structural support for the cell; they help to pull chromosomes apart during cell division; and they guide the trafficking of proteins and molecules across the cell. The building blocks of microtubules are proteins called αβ-tubulin, which are continually added to and removed from the ends of a microtubule, causing it to grow and shrink. Other proteins that interact with the microtubules can help to speed up these construction and deconstruction processes. Ayaz et al. took a closer look at the structure of one particular family of proteins that make it easier for the microtubules to grow, using a technique called X-ray crystallography. The resulting images show two sites—called TOG1 and TOG2—on the enzymes that attach to the αβ-tubulin proteins. Ayaz et al. found that this binding can only occur when αβ-tubulin has a curved shape, which only happens when the tubulins are not included in, or are only bound weakly to the end of, a microtubule. Previous research suggested that the two binding sites might work together to provide ‘scaffolding’ that stabilizes the microtubule. However, genetic experiments by Ayaz et al. show that microtubules will grow even if one of the binding sites is missing. Both TOG1 and TOG2 bind to αβ-tubulin in the same way, and by using computer simulations Ayaz et al. found that this helps to speed up the growth of microtubules. This is because the enzyme's two sites concentrate the individual tubulin building blocks at the ends of the filament. For example, TOG2 could bind to the end of the microtubule, while TOG1 holds an αβ-tubulin protein nearby and ready to bind to the filament's end. This tethering allows the microtubules to be assembled more efficiently.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.03069

DOI: 10.7554/eLife.03069.001

DOI: 10.7554/eLife.03069.002

DOI: 10.7554/eLife.03069.003

DOI: 10.7554/eLife.03069.004

DOI: 10.7554/eLife.03069.005

DOI: 10.7554/eLife.03069.006

DOI: 10.7554/eLife.03069.007

DOI: 10.7554/eLife.03069.008

DOI: 10.7554/eLife.03069.009

DOI: 10.7554/eLife.03069.010

DOI: 10.7554/eLife.03069.011

DOI: 10.7554/eLife.03069.012

DOI: 10.7554/eLife.03069.013

DOI: 10.7554/eLife.03069.014

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2014

detail.hit.zdb_id: 2687154-3

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