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How the dyes affect folding of small proteins in single-molecule FRET experiments : A simulation study. / Chekmarev, Sergei F.

In: Biophysical Chemistry, Vol. 254, 106243, 01.11.2019, p. 106243.

Research output: Contribution to journal › Article › peer-review

Harvard

Chekmarev, SF 2019, 'How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study', Biophysical Chemistry, vol. 254, 106243, pp. 106243. https://doi.org/10.1016/j.bpc.2019.106243

APA

Chekmarev, S. F. (2019). How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study. Biophysical Chemistry, 254, 106243. [106243]. https://doi.org/10.1016/j.bpc.2019.106243

Vancouver

Chekmarev SF. How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study. Biophysical Chemistry. 2019 Nov 1;254:106243. 106243. Epub 2019 Aug 9. doi: 10.1016/j.bpc.2019.106243

Author

Chekmarev, Sergei F. / How the dyes affect folding of small proteins in single-molecule FRET experiments : A simulation study. In: Biophysical Chemistry. 2019 ; Vol. 254. pp. 106243.

BibTeX

@article{7b996bc9fadc46cb99263fcc44aa1b34,
title = "How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study",
abstract = "A key question in the application of the single-molecule F{\"o}rster resonance energy transfer (smFRET) technique to study protein folding is how the dyes affect the protein behavior. Understanding of these effects is particularly important for small proteins, for which the dyes, along with their linkers, can be comparable in size (mass) with the protein. Using a coarse-grained model, we simulated folding of BBL protein and two of its FRET constructs. The obtained results suggest that even for small proteins, such as the 45-residue BBL, the appearance of the excluded volume in the protein conformation space due to the presence of dyes does not change the overall picture of folding. At the same time, some deviations from folding of the original protein are observed, in particular, the FRET constructs fold considerably slower than the original protein because the protein collapse in the initial state of folding is slowed down due to the protein loading with relatively massive dyes.",
keywords = "Dye positions, Folding times, Free energy surfaces, FRET efficiency histograms, Protein folding, Single-molecule F{\"o}rster resonance energy transfer (smFRET), Single-molecule Forster resonance energy transfer (smFRET), SPECTROSCOPY, DISTANCES, DYNAMICS, STATE, MECHANISMS",
author = "Chekmarev, {Sergei F.}",
note = "Copyright {\textcopyright} 2019 Elsevier B.V. All rights reserved.",
year = "2019",
month = nov,
day = "1",
doi = "10.1016/j.bpc.2019.106243",
language = "English",
volume = "254",
pages = "106243",
journal = "Biophysical Chemistry",
issn = "0301-4622",
publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - How the dyes affect folding of small proteins in single-molecule FRET experiments

T2 - A simulation study

AU - Chekmarev, Sergei F.

N1 - Copyright © 2019 Elsevier B.V. All rights reserved.

PY - 2019/11/1

Y1 - 2019/11/1

N2 - A key question in the application of the single-molecule Förster resonance energy transfer (smFRET) technique to study protein folding is how the dyes affect the protein behavior. Understanding of these effects is particularly important for small proteins, for which the dyes, along with their linkers, can be comparable in size (mass) with the protein. Using a coarse-grained model, we simulated folding of BBL protein and two of its FRET constructs. The obtained results suggest that even for small proteins, such as the 45-residue BBL, the appearance of the excluded volume in the protein conformation space due to the presence of dyes does not change the overall picture of folding. At the same time, some deviations from folding of the original protein are observed, in particular, the FRET constructs fold considerably slower than the original protein because the protein collapse in the initial state of folding is slowed down due to the protein loading with relatively massive dyes.

AB - A key question in the application of the single-molecule Förster resonance energy transfer (smFRET) technique to study protein folding is how the dyes affect the protein behavior. Understanding of these effects is particularly important for small proteins, for which the dyes, along with their linkers, can be comparable in size (mass) with the protein. Using a coarse-grained model, we simulated folding of BBL protein and two of its FRET constructs. The obtained results suggest that even for small proteins, such as the 45-residue BBL, the appearance of the excluded volume in the protein conformation space due to the presence of dyes does not change the overall picture of folding. At the same time, some deviations from folding of the original protein are observed, in particular, the FRET constructs fold considerably slower than the original protein because the protein collapse in the initial state of folding is slowed down due to the protein loading with relatively massive dyes.

KW - Dye positions

KW - Folding times

KW - Free energy surfaces

KW - FRET efficiency histograms

KW - Protein folding

KW - Single-molecule Förster resonance energy transfer (smFRET)

KW - Single-molecule Forster resonance energy transfer (smFRET)

KW - SPECTROSCOPY

KW - DISTANCES

KW - DYNAMICS

KW - STATE

KW - MECHANISMS

UR - http://www.scopus.com/inward/record.url?scp=85070870645&partnerID=8YFLogxK

U2 - 10.1016/j.bpc.2019.106243

DO - 10.1016/j.bpc.2019.106243

M3 - Article

C2 - 31442765

AN - SCOPUS:85070870645

VL - 254

SP - 106243

JO - Biophysical Chemistry

JF - Biophysical Chemistry

SN - 0301-4622

M1 - 106243

ER -

ID: 21347170