The role of the protein matrix in green fluorescent protein fluorescence

Photochemistry and Photobiology
Scott L Maddalo, Marc Zimmer

Abstract

In the ground state of the highly conjugated green fluorescent protein (GFP), the chromophore should be planar. However, numerous crystal structures of GFP and GFP-like proteins have been reported with slightly twisted chromophores. We have previously shown that the protein cavity surrounding the chromophore in wild-type GFP is not complementary with a planar chromophore. This study shows that the crystal structure of wild-type GFP is not an anomaly: most of the GFP and GFP-like proteins in the protein databank have a protein matrix that is not complementary with a planar chromophore. When the pi-conjugation across the ethylenic bridge of the chromophore is removed the protein matrix will significantly twist the freely rotating chromophore from the relatively planar structures found in the crystal structures. The possible consequences of this nonplanar deformation on the photophysics of GFP are discussed. A volume analysis of the cis-trans-isomerization of HBDI, a GFP chromophore model compound, reveals that its hula-twist motion is volume conserving. This means that, if the GFP chromophore or GFP chromophore model compounds undergo a cis-trans-isomerization in a volume-constricting medium, such as a protein matrix or viscous l...Continue Reading

References

Dec 20, 1994·Proceedings of the National Academy of Sciences of the United States of America·R HeimR Y Tsien
Aug 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·M ChattorajS G Boxer
Nov 26, 1996·Proceedings of the National Academy of Sciences of the United States of America·H NiwaF I Tsuji
May 1, 1997·Nature Structural Biology·G J PalmA Wlodawer
Oct 1, 1996·Nature Biotechnology·F YangG N Phillips
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·W WeberP W Langhoff
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Dec 2, 2000·Nature Structural Biology·M A WallR Ranganathan
Feb 24, 2001·Proceedings of the National Academy of Sciences of the United States of America·D YarbroughS J Remington
Jun 2, 2001·The Journal of Biological Chemistry·O GriesbeckR Y Tsien
Jun 21, 2002·Nature·Dinshaw J Patel
May 6, 2003·Journal of Molecular Biology·Jae Hyun BaeNediljko Budisa
Aug 12, 2003·The Journal of Biological Chemistry·Jan PetersenJamie Rossjohn
Aug 29, 2003·Biophysical Journal·Anny Follenius-WundClaire Pigault
Oct 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·David P BarondeauElizabeth D Getzoff
Dec 20, 2003·Proceedings of the National Academy of Sciences of the United States of America·Rajul K Jain, Rama Ranganathan
Mar 27, 2004·Journal of Photochemistry and Photobiology. B, Biology·V SineshchekovA Sudnitsin
Apr 29, 2004·Journal of the American Chemical Society·María Elena MartinMassimo Olivucci
May 18, 2004·Proteins·Atsushi YamadaTakahisa Yamato
Sep 2, 2004·Photochemistry and Photobiology·Jared V GoldstoneBettina M Voelker
Dec 8, 2004·Nature Biotechnology·George H Patterson
Dec 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·John T M KennisRienk van Grondelle
Feb 1, 2005·FEBS Letters·Roger Y Tsien
Mar 9, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·G ChiricoF Beltram

❮ Previous
Next ❯

Citations

Aug 25, 2011·Accounts of Chemical Research·Laren M TolbertKyril M Solntsev
Nov 5, 2010·The Journal of Physical Chemistry. B·Alex A SammaMarc Zimmer
Aug 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Benjamin T AndrewsPatricia A Jennings
May 20, 2009·The Journal of Chemical Physics·Seth Olsen, Ross H McKenzie
Jul 27, 2011·The Journal of Chemical Physics·Artur Nenov, Regina de Vivie-Riedle
Jul 7, 2009·Journal of Molecular Biology·Benjamin T AndrewsPatricia A Jennings
Sep 8, 2007·Journal of Molecular Biology·Benjamin T AndrewsPatricia A Jennings
Mar 17, 2016·The Journal of Physical Chemistry Letters·Longteng TangChong Fang
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Gurpreet Singh SandhuJeffrey L Duerk
Oct 29, 2009·Biochemical and Biophysical Research Communications·B S MelnikT N Melnik
Oct 28, 2014·PloS One·Olesya V StepanenkoKonstantin K Turoverov
Jan 15, 2009·Journal of the American Chemical Society·Jian DongLaren M Tolbert
Mar 26, 2013·The Journal of Physical Chemistry Letters·Benjamin T AndrewsPatricia A Jennings
Jan 21, 2010·Journal of the American Chemical Society·Anthony BaldridgeLaren M Tolbert
Oct 15, 2011·The Journal of Physical Chemistry. a·Shahnawaz RafiqGurunath Ramanathan
Sep 24, 2016·Journal of the American Chemical Society·Jae Woo Park, Young Min Rhee
Oct 19, 2016·Chemical Reviews·Atanu AcharyaAnna I Krylov
Jan 12, 2017·Biochemistry·Shounak BanerjeeChristopher Bystroff
Jan 16, 2016·Physical Chemistry Chemical Physics : PCCP·Jae Woo Park, Young Min Rhee
Sep 23, 2009·Chemical Society Reviews·Timothy D Craggs
Sep 9, 2011·PloS One·Marco ConstanteMark Isalan
Sep 24, 2013·Chemical Society Reviews·Karin Nienhaus, G Ulrich Nienhaus
Mar 9, 2010·Bioorganicheskaia khimiia·P E IvashkinK A Luk'ianov
Jan 4, 2020·Science·Matthew G RomeiSteven G Boxer
Feb 8, 2011·Molecular BioSystems·Wayne J-H OngMarc Zimmer
Mar 13, 2012·Physical Chemistry Chemical Physics : PCCP·Arnfinn Hykkerud SteindalJacob Kongsted
Dec 21, 2013·Physical Chemistry Chemical Physics : PCCP·Jan Boyke Schönborn, Bernd Hartke
Dec 11, 2008·The Journal of Physical Chemistry. B·Colleen M MegleyMarc Zimmer
Nov 10, 2020·Advances in Colloid and Interface Science·Jia KongZhimin He
Oct 2, 2008·Journal of the American Chemical Society·Jian DongLaren M Tolbert
Aug 6, 2020·Journal of Photochemistry and Photobiology. A, Chemistry·Matthew G RomeiSteven G Boxer
Jan 28, 2011·The Journal of Physical Chemistry. B·Jamie ConyardStephen R Meech
Mar 15, 2011·Langmuir : the ACS Journal of Surfaces and Colloids·Anthony BaldridgeLaren M Tolbert
Jun 14, 2011·Journal of Chemical Theory and Computation·Gabriella JonassonIsabelle Demachy
Jan 13, 2018·Journal of the American Chemical Society·Lena SiminePeter J Rossky

❮ Previous
Next ❯

Software Mentioned

MacroModel
AMBER

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.