Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle

Julian M. Schmidt-Engler, Larissa Blankenburg, Bartosz Błasiak, Luuk J.G.W. Van Wilderen, Minhaeng Cho, Jens Bredenbeck

Research output: Contribution to journalArticle

Abstract

The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.

Original languageEnglish
JournalAnalytical Chemistry
DOIs
Publication statusAccepted/In press - 2019 Jan 1

Fingerprint

Solvation
Labels
Proteins
Intrinsically Disordered Proteins
Protein folding
Absorption spectroscopy
Sulfur
Ground state
Stretching
Infrared spectroscopy
Membrane Proteins
Chemical activation
Pumps
Atoms
Water
Sensors

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle. / Schmidt-Engler, Julian M.; Blankenburg, Larissa; Błasiak, Bartosz; Van Wilderen, Luuk J.G.W.; Cho, Minhaeng; Bredenbeck, Jens.

In: Analytical Chemistry, 01.01.2019.

Research output: Contribution to journalArticle

Schmidt-Engler, Julian M. ; Blankenburg, Larissa ; Błasiak, Bartosz ; Van Wilderen, Luuk J.G.W. ; Cho, Minhaeng ; Bredenbeck, Jens. / Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle. In: Analytical Chemistry. 2019.
@article{8cef9eb64e0b4ee2b187a3c66c5eaea0,
title = "Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle",
abstract = "The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.",
author = "Schmidt-Engler, {Julian M.} and Larissa Blankenburg and Bartosz Błasiak and {Van Wilderen}, {Luuk J.G.W.} and Minhaeng Cho and Jens Bredenbeck",
year = "2019",
month = "1",
day = "1",
doi = "10.1021/acs.analchem.9b03997",
language = "English",
journal = "Analytical Chemistry",
issn = "0003-2700",

}

TY - JOUR

T1 - Vibrational Lifetime of the SCN Protein Label in H2O and D2O Reports Site-Specific Solvation and Structure Changes during PYP's Photocycle

AU - Schmidt-Engler, Julian M.

AU - Blankenburg, Larissa

AU - Błasiak, Bartosz

AU - Van Wilderen, Luuk J.G.W.

AU - Cho, Minhaeng

AU - Bredenbeck, Jens

PY - 2019/1/1

Y1 - 2019/1/1

N2 - The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.

AB - The application of vibrational labels such as thiocyanate »(-S-CN) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy. Due to the insulating effect of the heavy sulfur atom in the case of the SCN label, the lifetime of the CN oscillator is expected to be particularly sensitive to its surrounding as it is not dominated by through-bond relaxation. We therefore investigate the vibrational lifetime of the SCN label at various positions in the blue light sensor protein Photoactive Yellow Protein (PYP) in the ground state and signaling state of the photoreceptor. We find that the vibrational lifetime of the CN stretching mode is strongly affected both by its protein environment and by the degree of exposure to the solvent. Even for label positions where the line shape and wavenumber observed by FTIR are barely changing upon activation of the photoreceptor, we find that the lifetime can change considerably. To obtain an unambiguous measure for the solvent exposure of the labeled site, we show that it is imperative to compare the lifetimes in H2O and D2O. Importantly, the lifetimes shorten in H2O as compared to D2O for water exposed labels, while they stay largely the same for buried labels. We quantify this effect by defining a solvent exclusion coefficient (SEC). The response of the label's vibrational lifetime to its solvent exposure renders it a suitable universal probe for protein investigations. This applies even to systems that are otherwise hard to address, such as transient or short-lived states, which could be created during a protein's working cycle (as here in PYP) or during protein folding. It is also applicable to flexible systems (intrinsically disordered proteins), protein-protein and protein-membrane interactions.

UR - http://www.scopus.com/inward/record.url?scp=85076751932&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85076751932&partnerID=8YFLogxK

U2 - 10.1021/acs.analchem.9b03997

DO - 10.1021/acs.analchem.9b03997

M3 - Article

C2 - 31769286

AN - SCOPUS:85076751932

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

ER -