A direct comparison of azide and nitrile vibrational probes

Gai, Xin; Coutifaris, Basil A.; Brewer, Scott H.; Fenlon, Edward E.

doi:10.1039/c0cp02774j

Cited by 58 publications

(96 citation statements)

References 59 publications

(132 reference statements)

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“…15,24,25 For example; its lifetime increases 2-fold in going from water to methanol. 23 In a nanometer-sized reverse micelle, its lifetime in the interfacial region, where the availability of H-bond donor to an azide group is scarce, is significantly longer than that in the core region of bulk type water environment.…”

Section: The Journal Of Physical Chemistry Lettersmentioning

confidence: 98%

Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes

Verma

Lee

Park

et al. 2015

J. Phys. Chem. Lett.

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Osmolytes are an integral part of living organism, e.g., the kidney uses sorbitol, trimethylglycine, taurine and myo-inositol to counter the deleterious effects of urea and salt. Therefore, knowing that the osmolytes' act either directly to the protein or mediated through water is of great importance. Our experimental and computational results show that protecting osmolytes, e.g., trimethylglycine and sorbitol, significantly modulate the water H-bonding network structure, although the magnitude and spatial extent of osmolyte-induced perturbation greatly vary. In contrast, urea behaves neutrally toward local water H-bonding network. Protecting osmolytes studied here show strong concentration-dependent behaviors (vibrational frequencies and lifetimes of two different infrared (IR) probes), while denaturant does not. The H-bond donor and/or acceptor (OH/NH) in a given osmolyte molecule play a critical role in defining their action. Our findings highlight the significance of the alteration of H-bonding network of water under biologically relevant environment, often encountered in real biological systems.

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Section: The Journal Of Physical Chemistry Lettersmentioning

confidence: 98%

Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes

Verma

Lee

Park

et al. 2015

J. Phys. Chem. Lett.

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“…1–10 In particular, ultrafast measurements of the stretching mode of the nitrile group in a variety of biological systems have provided insight into site-specific vibrational dynamics. 11–17 Since both the N 3 and CN transitions are found in a spectrally transparent region of most biological molecules, several studies have benefited from the isolated and relatively sharp spectral feature to investigate beta-amyloid aggregation, drug-enzyme interactions, and other biological processes.…”

Section: Introductionmentioning

confidence: 99%

“…2, 12, 25–27 Both the N 3 transition and the CN transition have many similar spectral properties and a direct comparison of these probes has been documented using 2’-azido-5-cyano-2’-deoxyuridine (N 3 CNdU). 10 The changes in vibrational frequency resulting from hydrogen bonding and sensitivity to local electric field changes of both localized infrared transitions offer many advantages to studies of structural dynamics. 21, 24 Further studies have extended the application of these probes in nucleosides to infrared, 2D IR, and NMR experiments.…”

Section: Introductionmentioning

confidence: 99%

Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside

et al. 2016

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The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2’-azido-5-cyano-2’-deoxyuridine (N3CNdU) are examined by two-dimensional infrared spectroscopy (2D IR). At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength was determined from the off-diagonal anharmoncity to be 66 cm−1 for the molecular distance of ~7.9 Å based on a structural map generated for this model system. In addition, the frequency-frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.

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“…Based on solvent studies such redshifts are expected to result from reduced H bonding, [33,34] suggesting that the N 3 probes are not fully solvent exposed in the unfolded state. As the CÀD and CN absorptions at the same positions in the unfolded protein are virtually identical to those of the free amino acid, the protected environment must be unique to the azide probes.…”

mentioning

confidence: 98%

IR Probes of Protein Microenvironments: Utility and Potential for Perturbation

Adhikary¹,

Zimmermann²,

Dawson³

et al. 2014

ChemPhysChem

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A variety of IR-active moieties with absorptions that are distinct from those of proteins have been developed as probes of local protein environments, including carbon-deuterium bonds (CD), cyano groups (CN), and azides (N3 ); however, no systematic analysis of their utility in a protein has been published. Previously, we characterized the N-terminal Src homology 3 domain of the murine adapter protein Crk-II (nSH3) with CD bonds site-selectively incorporated throughout, and showed that it is relatively rigid and electrostatically heterogeneous and that it thermally unfolds under equilibrium conditions via a simple two-state mechanism. We now report the synthesis and characterization of eight variants of nSH3 with CN and/or N3 probes at five of the same positions. In agreement with previous studies, the position-dependent spectra suggest that both probes are predominantly sensitive to hydration, and not to their local electrostatic environments. Importantly, both probes also tend to significantly perturb the protein if they are not incorporated at surface-exposed positions. Thus, unlike CD labels, which are both sensitive to their environment and non-perturbative, CN and N3 probes should be used with caution.

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A direct comparison of azide and nitrile vibrational probes

Cited by 58 publications

References 59 publications

Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes

Modulation of the Hydrogen Bonding Structure of Water by Renal Osmolytes

Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside

IR Probes of Protein Microenvironments: Utility and Potential for Perturbation

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