Tracking carrier protein motions with Raman spectroscopy

Epstein, Samuel C.; Huff, Adam R.; Winesett, Emily S.; Londergan, Casey H.; Charkoudian, Louise K.

doi:10.1038/s41467-019-10184-2

Cited by 20 publications

(22 citation statements)

References 29 publications

(36 reference statements)

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“…The Raman peaks at 550-682 cm −1 region were assigned to represent disulfide conformations, whilst the 867-797 cm −1 ones were assigned to represent the hydrogen bonding state of tyrosine residues. Also, the significant shift in Raman spectrum peak to 1630 cm −1 can be attributed to the presence of tertiary structure of the immobilized antibody [45] (Fig. 8c).…”

Section: Morphological Evaluation Of Carbon Quantum Dots and Its Nanomentioning

confidence: 89%

New Immunosensing-Fluorescence Detection of Tumor Marker Cytokeratin-19 Fragment (CYFRA 21-1) Via Carbon Quantum Dots/Zinc Oxide Nanocomposite

2020

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The rapid detection of lung cancer in early stages using the antigen cytokeratin-19 fragment (CYFRA 21-1) as a tumor marker in human serum plays an important role in the survival of patients and taking a fast surgical reaction. This study aimed to employ the green synthesized carbon quantum dots conjugated zinc oxide nanocomposite as a highly sensitive fluorescence immunosensing solution for fast determination of CYFRA 21-1 antigen in human serum. The suggested method was conducted by applying a hydrothermal method to prepare carbon quantum dots using Citrus lemon pericarp. The formed carbon quantum dots were used in the reduction and stabilization of zinc acetate to synthesize carbon quantum dots-zinc oxide nanocomposite. To form a sandwich capping antibodyantigen-antibody immunosensing system, a CYFRA 21-1 antigen was trapped by immobilizing a non-conjugated monoclonal antibody BM 19.21 on the surface of carbon quantum dots-zinc oxide nanocomposite and another monoclonal antibody KS 19.1, which was coated on the microtiter well surface. This system has a tunable fluorescence feature recorded at excitation and emission of λ ex = 470 and λ em = 520 nm, respectively. The suggested nanocomposite fluorescence immunosensing system displayed a linear relationship of 0.01-100 ng mL −1 with a limit of detection of 0.008 ng mL −1. The suggested immunosensing system based on carbon quantum dots-zinc oxide nanocomposite provides a promising approach for rapid diagnoses of lung cancer by detecting CYFRA 21-1 in human serum.

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Section: Morphological Evaluation Of Carbon Quantum Dots and Its Nanomentioning

confidence: 89%

New Immunosensing-Fluorescence Detection of Tumor Marker Cytokeratin-19 Fragment (CYFRA 21-1) Via Carbon Quantum Dots/Zinc Oxide Nanocomposite

2020

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“…5 A ) to enable the rapid characterization of ACP chain sequestration via Raman spectroscopy ( Fig. 6 ) ( 74 ). In this approach, holo -ACPs are converted into probe-labeled crypto -ACPs through the AasS ligase-catalyzed loading of alkyne-containing carboxylic acid substrates onto the terminal thiol of the Ppant arm.…”

Section: Chemical Probes Enable Deeper Insight Into Type II Pks Acp Smentioning

confidence: 99%

“…The terminal alkyne probe enables the rapid visualization of the molecular cargo’s local environment using Raman spectroscopy. The intrinsic timescale of Raman spectroscopy for the alkyne probe is about 10 picoseconds, so any configurations that interconvert more slowly can be distinguished by spectral line shape ( 74 ). Our research team characterized the chain sequestration behaviors of six ACPs, including two type II PKS ACPs that had not been previously structurally characterized (from the benastatin and arimetamycin biosynthetic pathways).…”

Section: Chemical Probes Enable Deeper Insight Into Type II Pks Acp Smentioning

confidence: 99%

“…The alkyne triple bond reports on the solvation environment (lower frequency when the probe experiences an aqueous environment or higher frequency when the probe experiences a hydrophobic environment, like the inside of the ACP helical bundle). The line shape reports on the picosecond-resolved range of conformations (data shown from octanoyl -AcpP, which sequesters its cargo, versus octanoyl -ratACP, which does not sequester its cargo) ( 74 ). ACP, acyl carrier protein; PKS, polyketide synthase.…”

Section: Chemical Probes Enable Deeper Insight Into Type II Pks Acp Smentioning

confidence: 99%

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Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways

Sulpizio¹,

Crawford²,

Koweek³

et al. 2021

Journal of Biological Chemistry

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Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing ‘unnatural natural products.’ Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.

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“…power radiated is the surface integral of S over a sphere of radius r, and hence we get[6], associated with this field, then we can write, = ℏ . ( 3 1 ) Between Eqns (30). and (31), we get, method of calculating the energy, U, associated with the electric field will be to calculate the work done by the electricfield in the displacement of the charge say Q, i.e.,…”

mentioning

confidence: 99%

Effect of the Oscillating Electric Field Due to the Oscillating Electric Dipole on Raman Lines

Kapil

Gilbert

2019

EEJP

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Raman Effect is the measurement of the intensity and wavelength of the inelastically scattered radiation that falls on a molecule. The electric field of the incident radiation polarizes the molecule on which it falls and this leads to the creation of an oscillating dipole. The incident polarized laser light is inelastically scattered by the molecular sample. The scattered light contains modified wavelengths called the Stokes and anti-Stokes lines or wavelengths. The oscillating electric dipole, created by the incident radiation, creates an oscillating electric field around it. Since the oscillating electric field of the incident radiation creates an oscillating electric dipole that create an oscillating electric field around it, it was surmised that this oscillating electric field can affect the frequency of vibration or oscillation of the oscillating electric dipole that produces it. This novel effect will change the frequency (frequencies) of the scattered radiation resulting in Stokes and anti-Stokes lines with modified frequencies. This theoretical research and its importance can be understood like this. For instance, if there are two cells or molecules, side by side, in which one is a healthy cell and the other is cancerous, or two different types of molecules are sitting side by side, this types of scattering should be able to distinguish one from the other since the Stokes and anti-Stokes lines from the two molecules will not be identical. Thus, the incident radiation of angular frequency ω1 polarizes the charges of the molecule on which it falls and this leads to the creation of an oscillating dipole of frequency ω2. The oscillating dipole creates an oscillating electric field that can create additional frequency of the oscillating dipole that created it, and let this be ωD. Then the Raman lines can have frequencies (ω1+ω2+ωD), (ω1+ω2-ωD), (ω1-ω2+ωD), and (ω1-ω2-ωD). Depending on the relative magnitudes of ω2 and ωD, Raman lines will be designated as Stokes and Anti-Stokes lines. Due to the law of conservation of energy, ωD will be less than ω2 since an oscillating dipole cannot create field of frequency more than its own frequency. Hence the frequencies (ω1-ω2+ωD) and (ω1-ω2-ωD) correspond to Stokes lines, and frequencies. (ω1+ω2+ωD) and (ω1+ω2‑ωD) will correspond to Anti-Stokes lines. Calculations for Stokes and Anti-stokes lines have been done for some molecules, namely Ammonia compound (NH3), Nitrousoxide compound (N2O), Water (H2O), Sulphur dioxide compound (SO2), Ozone compound (O3). Calculations have also been done for compounds containing carbon, such as Dichloromethane compound (CH4Cl2), Formic acid compound (CH2O2), Methanol compound (CH4O), Benzene compound (C6H6), Propane compound (C3H8), and Carbonyl chloride compound (Cl2CO). The theory developed predicts new phenomena of getting Stokes and anti-Stokes lines with modified wavelengths which have not been observed experimentally as of to-day.

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Tracking carrier protein motions with Raman spectroscopy

Cited by 20 publications

References 29 publications

New Immunosensing-Fluorescence Detection of Tumor Marker Cytokeratin-19 Fragment (CYFRA 21-1) Via Carbon Quantum Dots/Zinc Oxide Nanocomposite

New Immunosensing-Fluorescence Detection of Tumor Marker Cytokeratin-19 Fragment (CYFRA 21-1) Via Carbon Quantum Dots/Zinc Oxide Nanocomposite

Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways

Effect of the Oscillating Electric Field Due to the Oscillating Electric Dipole on Raman Lines

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