The precious fluorine on the ring: fluorine NMR for biological systems

Boeszoermenyi, Andras; Ogórek, Barbara; Jain, Akshay; Arthanari, Haribabu; Wagner, Gerhard

doi:10.1007/s10858-020-00331-z

Cited by 37 publications

(33 citation statements)

References 117 publications

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“…DNA and RNA secondary and tertiary structure 19 F NMR spectroscopy also represents a useful analytical approach to study the structure, function and molecular dynamics of nucleic acids [89]. Following early advances by Micura and co-workers in the late 2000s that investigated the suitability of 19 F NMR for the conformational analysis of single and double helix RNA strands [90][91][92][93] 19 F NMR has found a particularly rich niche of applications in the conformational analysis of higher-ordered DNA and RNA G-quadruplex structures.…”

Section: F Nmrmentioning

confidence: 99%

¹⁹F NMR as a tool in chemical biology

Giménez¹,

Phelan²,

Murphy³

et al. 2021

Beilstein J. Org. Chem.

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We previously reviewed the use of 19F NMR in the broad field of chemical biology [Cobb, S. L.; Murphy, C. D. J. Fluorine Chem. 2009, 130, 132–140] and present here a summary of the literature from the last decade that has the technique as the central method of analysis. The topics covered include the synthesis of new fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein–protein interactions, protein–ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate biosynthesis and biodegradation of fluorinated organic compounds is also described.

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Section: F Nmrmentioning

confidence: 99%

¹⁹F NMR as a tool in chemical biology

Giménez¹,

Phelan²,

Murphy³

et al. 2021

Beilstein J. Org. Chem.

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“…In addition, the bioorthogonality of fluorine atoms facilitates their use for biomolecular and biological samples, especially in the context of "exchange-based" small molecule screening against biomolecular targets inside membrane-less organelles. 28,31,32 The efficacy of drug candidates against biomolecular targets crucially relies on their pharmacokinetic properties ensuring their bio-availability. 33 Similar to the case of biomolecules located inside membrane-bound organelles, drugs have to be able to efficiently enter the phase separated membrane-less compartment.…”

Section: Articlementioning

confidence: 99%

Dynamical component exchange in a model phase separating system: an NMR-based approach

Pantoja

Zweckstetter

Rezaei‐Ghaleh

2022

Phys. Chem. Chem. Phys.

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“…One approach to enhance NMR sensitivity is by introducing an 19 F probe at a specific residue (6,18), which unfortunately forgoes residue-specific details of protein-crowder and proteinprotein interactions.…”

Section: Significance Statementmentioning

confidence: 99%

“…However, kinetic properties are best characterized by the observation, not the absence, of NMR signals. One approach to enhance NMR sensitivity is by introducing an 19 F probe at a specific residue (6, 18), which unfortunately forgoes residue-specific details of protein-crowder and protein-protein interactions.…”

mentioning

confidence: 99%

Preferential interactions of a crowder protein with the specific binding site of a native protein complex

Qin

Gong

et al. 2021

Preprint

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The crowded cellular environments provide ample opportunities for proteins to interact with bystander macromolecules, yet direct evidence, let alone residue-specific information, for such nonspecific binding is rare. Here, by combining NMR spectroscopy and atomistic modeling, we investigated how crowders influence the association equilibrium and kinetics of two protein partners, EIN and HPr. Ficoll-70 increases the EIN-HPr binding affinity whereas bovine serum albumin (BSA) decreases the affinity. The opposite effects of the two crowders are quantitatively explained by atomistic modeling, which shows that the stabilizing effect of Ficoll-70 arises from volume exclusion favoring the bound state. In contrast, the destabilizing effect of BSA arises from preferential soft interactions with the free state; notably, BSA has favorable electrostatic interactions with positively charged HPr residues within the EIN-binding site. Some of the residues from this site indeed experience significant chemical shift perturbation when titrated with BSA, while the relaxation rates of HPr backbone amides exhibit overall elevation. Furthermore, relaxation dispersion data indicate that Ficoll-70 and BSA both slow down the EIN-HPr association rate, but change the dissociate rate in opposite directions. The observations on kinetics are accounted for by two effects of the crowders: increasing the solution microviscosity and reshaping the EIN-HPr interaction energy surface. The kind of preferential interactions between BSA and HPr that leads to competition with EIN should be prevalent in cellular environments. Our NMR results and atomistic modeling provide benchmarks, at both qualitative and quantitative levels, for the effects of crowded cellular environments on protein-protein specific interactions.

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The precious fluorine on the ring: fluorine NMR for biological systems

Cited by 37 publications

References 117 publications

¹⁹F NMR as a tool in chemical biology

¹⁹F NMR as a tool in chemical biology

Dynamical component exchange in a model phase separating system: an NMR-based approach

Preferential interactions of a crowder protein with the specific binding site of a native protein complex

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The precious fluorine on the ring: fluorine NMR for biological systems

Cited by 37 publications

References 117 publications

19F NMR as a tool in chemical biology

19F NMR as a tool in chemical biology

Dynamical component exchange in a model phase separating system: an NMR-based approach

Preferential interactions of a crowder protein with the specific binding site of a native protein complex

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¹⁹F NMR as a tool in chemical biology

¹⁹F NMR as a tool in chemical biology