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Accumulation of storage proteins in plant seeds is mediated by amyloid formation

Antonets, Kirill S. ; Belousov, Mikhail V. ; Sulatskaya, Anna I. ; [et al.]

Public Library of Science (PLoS) ; 2020

In: PLOS Biology Vol. 18, No. 7 ( 2020-7-23), p. e3000564-

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In: PLOS Biology, Public Library of Science (PLoS), Vol. 18, No. 7 ( 2020-7-23), p. e3000564-

Type of Medium: Online Resource

ISSN: 1545-7885

URL: Article

DOI: 10.1371/journal.pbio.3000564

DOI: 10.1371/journal.pbio.3000564.g001

DOI: 10.1371/journal.pbio.3000564.g002

DOI: 10.1371/journal.pbio.3000564.g003

DOI: 10.1371/journal.pbio.3000564.g004

DOI: 10.1371/journal.pbio.3000564.g005

DOI: 10.1371/journal.pbio.3000564.g006

DOI: 10.1371/journal.pbio.3000564.s001

DOI: 10.1371/journal.pbio.3000564.s002

DOI: 10.1371/journal.pbio.3000564.s003

DOI: 10.1371/journal.pbio.3000564.s004

DOI: 10.1371/journal.pbio.3000564.s005

DOI: 10.1371/journal.pbio.3000564.s006

DOI: 10.1371/journal.pbio.3000564.s007

DOI: 10.1371/journal.pbio.3000564.s008

DOI: 10.1371/journal.pbio.3000564.s009

DOI: 10.1371/journal.pbio.3000564.s010

DOI: 10.1371/journal.pbio.3000564.s011

DOI: 10.1371/journal.pbio.3000564.s012

DOI: 10.1371/journal.pbio.3000564.s013

DOI: 10.1371/journal.pbio.3000564.s014

DOI: 10.1371/journal.pbio.3000564.s015

DOI: 10.1371/journal.pbio.3000564.s016

DOI: 10.1371/journal.pbio.3000564.s017

DOI: 10.1371/journal.pbio.3000564.s018

DOI: 10.1371/journal.pbio.3000564.r001

DOI: 10.1371/journal.pbio.3000564.r002

DOI: 10.1371/journal.pbio.3000564.r003

DOI: 10.1371/journal.pbio.3000564.r004

DOI: 10.1371/journal.pbio.3000564.r005

DOI: 10.1371/journal.pbio.3000564.r006

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2020

detail.hit.zdb_id: 2126773-X

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Near-infrared bioluminescent proteins for two-color multimodal imaging

Rumyantsev, Konstantin A. ; Turoverov, Konstantin K. ; Verkhusha, Vladislav V.

Springer Science and Business Media LLC ; 2016

In: Scientific Reports Vol. 6, No. 1 ( 2016-11-11)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-11-11)

Abstract: Bioluminescence imaging became a widely used technique for noninvasive study of biological processes in small animals. Bioluminescent probes with emission in near-infrared (NIR) spectral region confer the advantage of having deep tissue penetration capacity. However, there are a very limited number of currently available luciferases that exhibit NIR bioluminescence. Here, we engineered two novel chimeric probes based on RLuc8 luciferase fused with iRFP670 and iRFP720 NIR fluorescent proteins. Due to an intramolecular bioluminescence resonance energy transfer (BRET) between RLuc8 and iRFPs, the chimeric luciferases exhibit NIR bioluminescence with maxima at 670 nm and 720 nm, respectively. The 50 nm spectral shift between emissions of the two iRFP chimeras enables combined multicolor bioluminescence imaging (BLI) and the respective multicolor fluorescence imaging (FLI) of the iRFPs. We show that for subcutaneously implanted cells, NIR bioluminescence provided a 10-fold increase in sensitivity compared to NIR FLI. In deep tissues, NIR BLI enabled detection of as low as 10 4 cells. Both BLI and FLI allowed monitoring of tumor growth and metastasis from early to late stages. Multimodal imaging, which combines concurrent BLI and FLI, provides continuous spatiotemporal analysis of metastatic cells in animals, including their localization and quantification.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/srep36588

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2615211-3

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Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

Rumyantsev, Konstantin A. ; Shcherbakova, Daria M. ; Zakharova, Natalia I. ; [et al.]

Springer Science and Business Media LLC ; 2015

In: Scientific Reports Vol. 5, No. 1 ( 2015-12-18)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2015-12-18)

Abstract: Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/srep18348

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 2615211-3

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Effect of Self-Association on the Structural Organization of Partially Folded Proteins: Inactivated Actin

Kuznetsova, Irina M. ; Biktashev, Alexander G. ; Khaitlina, Sofia Yu. ; [et al.]

Elsevier BV ; 1999

In: Biophysical Journal Vol. 77, No. 5 ( 1999-11), p. 2788-2800

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In: Biophysical Journal, Elsevier BV, Vol. 77, No. 5 ( 1999-11), p. 2788-2800

Type of Medium: Online Resource

ISSN: 0006-3495

URL: Article

DOI: 10.1016/S0006-3495(99)77111-0

Language: English

Publisher: Elsevier BV

Publication Date: 1999

detail.hit.zdb_id: 1477214-0

SSG: 12

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Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines

Nesterov, Semen V. ; Ilyinsky, Nikolay S. ; Plokhikh, Konstantin S. ; [et al.]

Elsevier BV ; 2024

In: International Journal of Biological Macromolecules Vol. 267 ( 2024-05), p. 131455-

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In: International Journal of Biological Macromolecules, Elsevier BV, Vol. 267 ( 2024-05), p. 131455-

Type of Medium: Online Resource

ISSN: 0141-8130

URL: Article

DOI: 10.1016/j.ijbiomac.2024.131455

Language: English

Publisher: Elsevier BV

Publication Date: 2024

detail.hit.zdb_id: 1483284-7

SSG: 12

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High Molecular Mass Crowders Change the Folding Pathway of D-Glucose/D-Galactose-Binding Protein

Fonin, Alexander V. ; Silonov, Serge A. ; Sitdikova, Asia K. ; [et al.]

Elsevier BV ; 2016

In: Biophysical Journal Vol. 110, No. 3 ( 2016-02), p. 213a-

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In: Biophysical Journal, Elsevier BV, Vol. 110, No. 3 ( 2016-02), p. 213a-

Type of Medium: Online Resource

ISSN: 0006-3495

URL: Article

DOI: 10.1016/j.bpj.2015.11.1182

Language: English

Publisher: Elsevier BV

Publication Date: 2016

detail.hit.zdb_id: 1477214-0

SSG: 12

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Intrinsically Disordered Proteins PH-Induced Structural Transitions in Overcrowded Milieu

Fonin, Alexander V. ; Asiya, Sitdikova K. ; Gagarskaia, Iuliia A. ; [et al.]

Elsevier BV ; 2018

In: Biophysical Journal Vol. 114, No. 3 ( 2018-02), p. 591a-

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In: Biophysical Journal, Elsevier BV, Vol. 114, No. 3 ( 2018-02), p. 591a-

Type of Medium: Online Resource

ISSN: 0006-3495

URL: Article

DOI: 10.1016/j.bpj.2017.11.3232

Language: English

Publisher: Elsevier BV

Publication Date: 2018

detail.hit.zdb_id: 1477214-0

SSG: 12

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Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure–function continuum with intrinsic disorder-based proteoforms

Fonin, Alexander V. ; Darling, April L. ; Kuznetsova, Irina M. ; [et al.]

Springer Science and Business Media LLC ; 2019

In: Cellular and Molecular Life Sciences Vol. 76, No. 22 ( 2019-11), p. 4461-4492

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In: Cellular and Molecular Life Sciences, Springer Science and Business Media LLC, Vol. 76, No. 22 ( 2019-11), p. 4461-4492

Type of Medium: Online Resource

ISSN: 1420-682X , 1420-9071

URL: Article

DOI: 10.1007/s00018-019-03276-1

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2019

detail.hit.zdb_id: 1458497-9

SSG: 12

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Ans Fluorescent Probe Induces Clustering of Amyloid Fibers

Sulatskaya, Anna I. ; Sulatsky, Maksim I. ; Povarova, Olga I. ; [et al.]

Elsevier BV ; 2021

In: Biophysical Journal Vol. 120, No. 3 ( 2021-02), p. 23a-

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In: Biophysical Journal, Elsevier BV, Vol. 120, No. 3 ( 2021-02), p. 23a-

Type of Medium: Online Resource

ISSN: 0006-3495

URL: Article

DOI: 10.1016/j.bpj.2020.11.402

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 1477214-0

SSG: 12

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Supplemental Information 2: Detailed procedure of protein expression and purification and a description of a determination of volume fraction of crowders

Stepanenko, Olesya V. ; Stepanenko, Olga V. ; Kuznetsova, Irina M. ; [et al.]

PeerJ ; 2019

In: PeerJ Vol. 7 ( 2019-04-08), p. e6707-

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In: PeerJ, PeerJ, Vol. 7 ( 2019-04-08), p. e6707-

Abstract: The exploring of biological processes in vitro under conditions of macromolecular crowding is a way to achieve an understanding of how these processes occur in vivo . In this work, we study the unfolding of the fluorescent probe iRFP713 in crowded environment in vitro . Previously, we showed that the unfolding of the dimeric iRFP713 is accompanied by the formation of a compact monomer and an intermediate state of the protein. In the intermediate state, the macromolecules of iRFP713 have hydrophobic clusters exposed to the surface of the protein and are prone to aggregation. Concentrated solutions of polyethylene glycol (PEG-8000), Dextran-40 and Dextran-70 with a molecular mass of 8000, 40000 and 70000 Da, respectively, were used to model the conditions for macromolecular crowding. A limited available space provided by all the crowding agents used favors to the enhanced aggregation of iRFP713 in the intermediate state at the concentration of guanidine hydrochloride (GdnHCl), at which the charge of protein surface is neutralized by the guanidine cations. This is in line with the theory of the excluded volume. In concentrated solutions of the crowding agents (240–300 mg/ml), the stabilization of the structure of iRFP713 in the intermediate state is observed. PEG-8000 also enhances the stability of iRFP713 in the monomeric compact state, whereas in concentrated solutions of Dextran-40 and Dextran-70 the resistance of the protein in the monomeric state against GdnHCl-induced unfolding decreases. The obtained data argues for the excluded volume effect being not the only factor that contributes the behavior of biological molecules in a crowded milieu. Crowding agents do not affect the structure of the native dimer of iRFP713, which excludes the direct interactions between the target protein and the crowding agents. PEGs of different molecular mass and Dextran-40/Dextran-70 are known to influence the solvent properties of water. The solvent dipolarity/polarizability and basicity/acidity in aqueous solutions of these crowding agents vary in different ways. The change of the solvent properties in aqueous solutions of crowding agents might impact the functioning of a target protein.

Type of Medium: Online Resource

ISSN: 2167-8359

URL: Article

DOI: 10.7717/peerj.6707

DOI: 10.7717/peerj.6707/fig-1

DOI: 10.7717/peerj.6707/fig-2

DOI: 10.7717/peerj.6707/fig-3

DOI: 10.7717/peerj.6707/fig-4

DOI: 10.7717/peerj.6707/fig-5

DOI: 10.7717/peerj.6707/fig-6

DOI: 10.7717/peerj.6707/fig-7

DOI: 10.7717/peerj.6707/fig-8

DOI: 10.7717/peerj.6707/fig-9

DOI: 10.7717/peerj.6707/table-1

DOI: 10.7717/peerj.6707/supp-1

DOI: 10.7717/peerj.6707/supp-2

Language: English

Publisher: PeerJ

Publication Date: 2019

detail.hit.zdb_id: 2703241-3

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