Structural prediction of a rhodamine-based biosensor and comparison with biophysical data

Literature Information

Publication Date 2012-12-17
DOI 10.1039/C2CP42396K
Impact Factor 3.676
Authors

Martin R. Webb, John E. T. Corrie


View Original

Abstract

The predicted structure has been calculated for a protein-based biosensor for inorganic phosphate (Pi), previously developed by some of us (Okoh et al., Biochemistry, 2006, 45, 14764). This is the phosphate binding protein from Escherichia coli labelled with two rhodamine fluorophores. Classical molecular dynamics and hybrid Car–Parrinello/molecular mechanics simulations allow us to provide molecular models of the biosensor both in the presence and in the absence of Pi. In the latter case, the rhodamine fluorophores maintain a stacked conformation in a ‘face A to face B’ orientation, which is different from the ‘face A to face A’ stacked orientation of free fluorophores in aqueous solution (Ilich et al., Spectrochim. Acta, Part A, 1996, 52, 1323). A protein conformation change upon binding Pi prevents significant stacking of the two rhodamines. In both states, the rhodamine fluorophores form hydrophobic contact with LEU291, without establishing significant hydrogen bonds with the protein. The accuracy of the models is established by a comparison between calculated and experimental absorption and circular dichroism spectra.

Related Literature

Front cover

Other

DOI: 10.1039/CS99625FX021

Correspondence

Other

DOI: 10.1039/AN884090151B

Analysts' certificates

Other

DOI: 10.1039/AN883080109A

Back matter

Other

DOI: 10.1039/CS99625BP025

Front cover

Cover

DOI: 10.1039/B7RP90014G

Contents pages

Other

DOI: 10.1039/CS97201FP009

Contents pages

Other

DOI: 10.1039/CS99423FP007

2004 : A year of growth and development

2003-12-10 Editorial

DOI: 10.1039/B315224N

You might also like

Compound Q&A

What is 3-Fluoro-2-methylbenzylamine (CAS: 771573-36-5)?

3-Fluoro-2-methylbenzylamine is an organic compound with the CAS number 771573-3...

771573-36-53-Fluoro-2-methylben...
Compound Q&A

Is Tert-butyl 2-(oxetan-3-ylidene)acetate (CAS: 1207175-03-8) safe?

Tert-butyl 2-(oxetan-3-ylidene)acetate is considered safe for its intended uses ...

1207175-03-8Tert-butyl 2-(oxetan...
Compound Q&A

What precautions should be taken when handling 4-Acetyl-2-fluorobenzonitrile (CAS: 214760-18-6)?

Proper personal protective equipment (PPE) such as gloves, goggles, and a lab co...

214760-18-64-Acetyl-2-fluoroben...
Compound Q&A

How is 2-Ethyl-4-methyl-1,3-thiazole (CAS: 15679-12-6) typically synthesized?

2-Ethyl-4-methyl-1,3-thiazole is commonly synthesized via the reaction of thiour...

15679-12-62-Ethyl-4-methyl-1,3...
Compound Q&A

How should 5',5''-([2,2'-Bithiophene]-5,5'-diyl)bis(([1,1':3',1''-terphenyl]-4,4''-dicarboxylic acid)) (CAS: 1227780-71-3) be stored?

This compound should be stored in a cool, dry place away from direct sunlight an...

1227780-71-35',5''''-([2,2'-Bith...
Compound Q&A

What regulatory guidelines apply to L-Lysine Acetate Salt (CAS: 52315-92-1)?

L-Lysine Acetate Salt (CAS: 52315-92-1) is subject to various regulatory guideli...

52315-92-1L-LYSINE ACETATE SAL...
Compound Q&A

Is 6-Fluoro-3-hydroxy-2-pyrazinecarboxamide (CAS: 259793-96-9) safe?

6-Fluoro-3-hydroxy-2-pyrazinecarboxamide (CAS: 259793-96-9) is generally conside...

259793-96-96-Fluoro-3-hydroxy-2...
Compound Q&A

What are the physical and chemical properties of 1,1'-Sulfonylbis(1H-imidazole) (CAS: 7189-69-7)?

1,1'-Sulfonylbis(1H-imidazole) is a crystalline solid with a molecular weight of...

7189-69-71,1'-Sulfonylbis(1H-...
Compound Q&A

What industries use 4-methyl-7-nitro-1H-indole-3-carbonitrile (CAS: 289483-82-5)?

4-Methyl-7-nitro-1H-indole-3-carbonitrile (CAS: 289483-82-5) is primarily used i...

289483-82-54-methyl-7-nitro-1H-...
Compound Q&A

How should waste containing 5-Bromo-3-indolyl-beta-galactoside (CAS: 97753-82-7) be handled?

Waste containing 5-Bromo-3-indolyl-beta-galactoside (CAS: 97753-82-7) should be ...

97753-82-75-Bromo-3-indolyl-be...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.