Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of
Haloalkane Dehalogenase Enzymes Dependent on the Choice of the
Chromophore?

J 2013

Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore?

AMARO, Mariana, Jan BREZOVSKÝ, Silvia KOVÁČOVÁ, Lukáš MAIER, Radka CHALOUPKOVÁ et. al.

Basic information

Original name

Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore?

Authors

AMARO, Mariana (620 Portugal), Jan BREZOVSKÝ (203 Czech Republic, belonging to the institution), Silvia KOVÁČOVÁ (703 Slovakia, belonging to the institution), Lukáš MAIER (203 Czech Republic, belonging to the institution), Radka CHALOUPKOVÁ (203 Czech Republic, belonging to the institution), Jan SYKORA (203 Czech Republic), Kamil PARUCH (203 Czech Republic, guarantor, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution) and Martin HOF (203 Czech Republic)

Edition

Journal of Physical Chemistry B, WASHINGTON, AMER CHEMICAL SOC, 2013, 1520-6106

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 3.377

RIV identification code

RIV/00216224:14310/13:00065798

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1021/jp403708c

UT WoS

000321542200006

Keywords in English

DYNAMIC STOKES SHIFT; WATER-PROTEIN FLUCTUATIONS; POLAR SOLVATION DYNAMICS; HYDRATION DYNAMICS; DIELECTRIC RESPONSE; SOLVENT RELAXATION; ACTIVE-SITE; SUBSTRATE; SURFACE; SIMULATIONS

Abstract

V originále

AB Time-dependent fluorescence shifts (TDFS) of chromophores selectively attached to proteins may give information on the dynamics of the probed protein moieties and their degree of hydration. Previously, we demonstrated that a coumarin dye selectively labeling the tunnel mouth of different haloalkane dehalogenases (HLDs) can distinguish between different widths of tunnel mouth openings. In order to generalize those findings analogous experiments were performed using a different chromophore probing the same region of these enzymes. To this end we synthesized and characterized three new fluorescent probes derived from dimethylaminonaphthalene bearing a linker almost identical to that of the coumarin dye used in our previous study. Labeling efficiencies, acrylamide quenching, fluorescence anisotropies, and TDFS for the examined fluorescent substrates confirm the picture gained from the coumarin studies: the different tunnel mouth opening, predicted by crystal structures, is reflected in the hydration and tunnel mouth dynamics of the investigated HLDs. Comparison of the TDFS reported by the coumarin dye with those obtained with the new dimethylaminonaphthalene dyes shows that the choice of chromophore may strongly influence the recorded TDFS characteristics. The intrinsic design of our labeling strategy and the variation of the linker length ensure that both dyes probe the identical enzyme region; moreover, the covalently fixed position of the chromophore does not allow for a major relocalization within the HLD structures. Our study shows, for the first time, that TDFS may strongly depend on the choice of the chromophore, even though the identical region of a protein is explored.

Links

CZ.1.05/2.1.00/01.0001, interní kód MU

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: CETOCOEN)

Investor: Ministry of Education, Youth and Sports of the CR, 2.1 Regional R&D Centres

GAP207/12/0775, research and development project

Name: Strukturně-funkční vztahy haloalkan dehalogenas

Investor: Czech Science Foundation

IAA401630901, research and development project

Name: Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami

Investor: Academy of Sciences of the Czech Republic, Evolution of substrate specificity in enzymes acting on xenobiotic compounds

Citovat

AMARO, Mariana, Jan BREZOVSKÝ, Silvia KOVÁČOVÁ, Lukáš MAIER, Radka CHALOUPKOVÁ, Jan SYKORA, Kamil PARUCH, Jiří DAMBORSKÝ and Martin HOF. Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2013, vol. 117, No 26, p. 7898-7906. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp403708c.

@article{1119352,
   author = {Amaro, Mariana and Brezovský, Jan and Kováčová, Silvia and Maier, Lukáš and Chaloupková, Radka and Sykora, Jan and Paruch, Kamil and Damborský, Jiří and Hof, Martin},
   article_location = {WASHINGTON},
   article_number = {26},
   doi = {http://dx.doi.org/10.1021/jp403708c},
   keywords = {DYNAMIC STOKES SHIFT; WATER-PROTEIN FLUCTUATIONS; POLAR SOLVATION DYNAMICS; HYDRATION DYNAMICS; DIELECTRIC RESPONSE; SOLVENT RELAXATION; ACTIVE-SITE; SUBSTRATE; SURFACE; SIMULATIONS},
   language = {eng},
   issn = {1520-6106},
   journal = {Journal of Physical Chemistry B},
   title = {Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore?},
   volume = {117},
   year = {2013}
}

TY  - JOUR
ID  - 1119352
AU  - Amaro, Mariana - Brezovský, Jan - Kováčová, Silvia - Maier, Lukáš - Chaloupková, Radka - Sykora, Jan - Paruch, Kamil - Damborský, Jiří - Hof, Martin
PY  - 2013
TI  - Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore?
JF  - Journal of Physical Chemistry B
VL  - 117
IS  - 26
SP  - 7898-7906
EP  - 7898-7906
PB  - AMER CHEMICAL SOC
SN  - 15206106
KW  - DYNAMIC STOKES SHIFT
KW  - WATER-PROTEIN FLUCTUATIONS
KW  - POLAR SOLVATION DYNAMICS
KW  - HYDRATION DYNAMICS
KW  - DIELECTRIC RESPONSE
KW  - SOLVENT RELAXATION
KW  - ACTIVE-SITE
KW  - SUBSTRATE
KW  - SURFACE
KW  - SIMULATIONS
N2  - AB Time-dependent fluorescence shifts (TDFS) of chromophores selectively attached to proteins may give information on the dynamics of the probed protein moieties and their degree of hydration. Previously, we demonstrated that a coumarin dye selectively labeling the tunnel mouth of different haloalkane dehalogenases (HLDs) can distinguish between different widths of tunnel mouth openings. In order to generalize those findings analogous experiments were performed using a different chromophore probing the same region of these enzymes. To this end we synthesized and characterized three new fluorescent probes derived from dimethylaminonaphthalene bearing a linker almost identical to that of the coumarin dye used in our previous study. Labeling efficiencies, acrylamide quenching, fluorescence anisotropies, and TDFS for the examined fluorescent substrates confirm the picture gained from the coumarin studies: the different tunnel mouth opening, predicted by crystal structures, is reflected in the hydration and tunnel mouth dynamics of the investigated HLDs. Comparison of the TDFS reported by the coumarin dye with those obtained with the new dimethylaminonaphthalene dyes shows that the choice of chromophore may strongly influence the recorded TDFS characteristics. The intrinsic design of our labeling strategy and the variation of the linker length ensure that both dyes probe the identical enzyme region; moreover, the covalently fixed position of the chromophore does not allow for a major relocalization within the HLD structures. Our study shows, for the first time, that TDFS may strongly depend on the choice of the chromophore, even though the identical region of a protein is explored.
ER  -

AMARO, Mariana, Jan BREZOVSKÝ, Silvia KOVÁČOVÁ, Lukáš MAIER, Radka CHALOUPKOVÁ, Jan SYKORA, Kamil PARUCH, Jiří DAMBORSKÝ and Martin HOF. Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2013, vol.~117, No~26, p.~7898-7906. ISSN~1520-6106. Available from: https://dx.doi.org/10.1021/jp403708c.

Detailed Information on Publication Record