Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics

Romesberg, Floyd E.

doi:10.1002/cbic.200300572

Cited by 13 publications

(14 citation statements)

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“…However, for a large protein molecule, site-specific detection is challenging, owing to the numerous similarities of intrinsic vibrational modes, making the spectra congested, broadened, and complicated. This problem can be alleviated by incorporating IR probes into proteins, endowing on them absorbance within the “transparent window” (1800–2500 cm –1 ). − Therefore, considerable attention has been devoted to the exploitation of ideal site-specific IR probes for protein systems.…”

Section: Introductionmentioning

confidence: 99%

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

et al. 2018

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Azido-modified aromatic amino acids have been used as powerful infrared probes for the site-specific detection of proteins because of their large transition dipole strengths. However, their complex absorption profiles hinder their wider application. The complicated absorption profile of 4-azido-l-phenylalanine (pNPhe) in isopropanol was identified and attributed to accidental Fermi resonances (FRs) by means of linear absorption and two-dimensional (2D) IR spectroscopies. The 2D IR results of pNPhe in HO and DO further demonstrate that the FRs are distinctively influenced by the hydrogen-bonding environment. Under the influence of FRs, the 2D IR shape is distorted, indicating that pNPhe is not a good candidate in spectral diffusion studies. A three-state model and first-principles calculations were used to analyze unperturbed energy levels, unveiling the FRs between the azide asymmetric stretching band and two combination bands. Furthermore, the anharmonic frequency calculations suggest that changing the substitution position of the azide group from para to meta can effectively modulate the FRs by reducing the coupling strength. This work provides a deep understanding of the FRs in azido-modified aromatic amino acids and sheds light on the modification of azido-modified amino acids for wider utilization as vibrational probes.

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Section: Introductionmentioning

confidence: 99%

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

et al. 2018

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“…Vibrational spectroscopy is a powerful technique for investigating biomolecular structure and dynamics. [1][2][3][4][5][6][7][8] Infrared (IR) studies of biomolecules are complementary to X-ray crystallography and nuclear magnetic resonance (NMR), two commonly employed techniques for biomolecular structure determination. X-Ray crystallography is an excellent method for high-resolution structure determination, but it does have limitations.…”

Section: Introductionmentioning

confidence: 99%

“…Features present in an IR absorption spectrum due to the probe can be traced back to a specific location in the biomolecule. Many examples of these types of IR probes have appeared in the literature; these include (but are not limited to) [20][21][22][23][24] isotopically labeled amide bonds, 1,6,[12][13][14] carbon-deuterium (C-D) bonds, 7,[57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72] azide, [73][74][75][76] and nitrile groups. [77][78][79][80][81][82][83][84][85][86][87][88][89][90][91][92][93] Historically, amide groups have been the most broadly utilized IR probe in biological experiments, and they continue to enjoy s...…”

Section: Introductionmentioning

confidence: 99%

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

Lindquist

Furse

Corcelli

2009

Phys. Chem. Chem. Phys.

148

164

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This paper presents an overview of recent experiments and theoretical developments aimed at using vibrational spectroscopy to understand the structure and dynamics of nitrile-labeled biomolecules. Nitrile groups are excellent vibrational probes of proteins and DNA because they absorb in a region of the spectrum that is relatively free of absorption due to the biomolecule, and they have high extinction coefficients. The vibrational frequency of nitrile groups is also extraordinarily sensitive to its local environment, and thus C[triple bond, length as m-dash]N bonds have been employed in both linear and 2-D infrared (IR) spectroscopy experiments and also as vibrational Stark probes of electric fields in proteins. The interpretation and design of these experiments would be enhanced by accurate calculations of IR spectra from molecular dynamics simulations. Recently, theoretical developments towards computing the vibrational spectrum of nitrile groups in the condensed-phase have been highly successful. A strong synergy between experiment and theory will further promote the use of vibrational spectroscopy of nitrile-labeled biomolecules to address fundamental questions of structure and dynamics that are elusive to other techniques.

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“…Therefore, IR probes with isotopic labels or a signal in the transparent window region between 1800 and 2500 cm –1 are used. 5 …”

Section: Introductionmentioning

confidence: 99%

“…However, IR spectral analysis of biomolecules is difficult because their IR signals often overlap with those of peptides. Therefore, IR probes with isotopic labels or a signal in the transparent window region between 1800 and 2500 cm –1 are used …”

Section: Introductionmentioning

confidence: 99%

TfNN¹⁵N: A γ-¹⁵N-Labeled Diazo-Transfer Reagent for the Synthesis of β-¹⁵N-Labeled Azides

et al. 2021

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Azides are infrared (IR) probes that are important for structure and dynamics studies of proteins. However, they often display complex IR spectra owing to Fermi resonances and multiple conformers. Isotopic substitution of azides weakens the Fermi resonance, allowing more accurate IR spectral analysis. Site-specifically 15 N-labeled aromatic azides, but not aliphatic azides, are synthesized through nitrosation. Both 15 N-labeled aromatic and aliphatic azides are synthesized through nucleophilic substitution or diazo-transfer reaction but as an isotopomeric mixture. We present the synthesis of TfNN 15 N, a γ- 15 N-labeled diazo-transfer reagent, and its use to prepare β- 15 N-labeled aliphatic as well as aromatic azides.

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Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics

Cited by 13 publications

References 100 publications

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

TfNN¹⁵N: A γ-¹⁵N-Labeled Diazo-Transfer Reagent for the Synthesis of β-¹⁵N-Labeled Azides

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Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics

Cited by 13 publications

References 100 publications

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

TfNN15N: A γ-15N-Labeled Diazo-Transfer Reagent for the Synthesis of β-15N-Labeled Azides

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Product

Resources

About

TfNN¹⁵N: A γ-¹⁵N-Labeled Diazo-Transfer Reagent for the Synthesis of β-¹⁵N-Labeled Azides