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Akoya Biosciences codex decay curve

At the mixing time of 250 ms, the bound state <t>CODEX</t> signal decays to 0.65 of the reference experiment (A, inset yellow); the decay rate fits to an inter-CF 3 distance of 13.6 ±3.0 Å, with the exponential decay fit curve of 0.5 * e −0.0053*t −0.5, matching the expected inter-dimer distance at the C-terminus of the parallel dimer (C). In contrast, the free state CODEX signal is almost the same as the reference experiment (A, inset blue) through all mixing times, corresponding to a large inter dimer distance at the C-terminus of more than 20 Å, agreeing with the anti-parallel dimer (B). Example <t>CODEX</t> <t>decay</t> curves at different inter fluorine distances are shown (A, grey). 30% of the bound state CitApc protein present in the citrate free sample caused the minor CODEX decay. The CODEX decay curve could be acquired beyond the 19 F T 1 of 321ms (Figure S10), thanks to an eight-fold DNP signal enhancement (Figure S9B).

Codex Decay Curve, supplied by Akoya Biosciences, used in various techniques. Bioz Stars score: 99/100, based on 12616 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 12616 article reviews

codex decay curve - by Bioz Stars, 2026-09

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1) Product Images from "Mechanism of sensor kinase CitA transmembrane signaling"

Article Title: Mechanism of sensor kinase CitA transmembrane signaling

Journal: bioRxiv

doi: 10.1101/2023.02.06.527302

At the mixing time of 250 ms, the bound state CODEX signal decays to 0.65 of the reference experiment (A, inset yellow); the decay rate fits to an inter-CF 3 distance of 13.6 ±3.0 Å, with the exponential decay fit curve of 0.5 * e −0.0053*t −0.5, matching the expected inter-dimer distance at the C-terminus of the parallel dimer (C). In contrast, the free state CODEX signal is almost the same as the reference experiment (A, inset blue) through all mixing times, corresponding to a large inter dimer distance at the C-terminus of more than 20 Å, agreeing with the anti-parallel dimer (B). Example CODEX decay curves at different inter fluorine distances are shown (A, grey). 30% of the bound state CitApc protein present in the citrate free sample caused the minor CODEX decay. The CODEX decay curve could be acquired beyond the 19 F T 1 of 321ms (Figure S10), thanks to an eight-fold DNP signal enhancement (Figure S9B).

Figure Legend Snippet: At the mixing time of 250 ms, the bound state CODEX signal decays to 0.65 of the reference experiment (A, inset yellow); the decay rate fits to an inter-CF 3 distance of 13.6 ±3.0 Å, with the exponential decay fit curve of 0.5 * e −0.0053*t −0.5, matching the expected inter-dimer distance at the C-terminus of the parallel dimer (C). In contrast, the free state CODEX signal is almost the same as the reference experiment (A, inset blue) through all mixing times, corresponding to a large inter dimer distance at the C-terminus of more than 20 Å, agreeing with the anti-parallel dimer (B). Example CODEX decay curves at different inter fluorine distances are shown (A, grey). 30% of the bound state CitApc protein present in the citrate free sample caused the minor CODEX decay. The CODEX decay curve could be acquired beyond the 19 F T 1 of 321ms (Figure S10), thanks to an eight-fold DNP signal enhancement (Figure S9B).

Techniques Used:

other:

Article Title: Mechanism of sensor kinase CitA transmembrane signaling
Article Snippet: An inter-CF 3 group distance shorter than about 20 Å is measurable by fitting the CODEX decay curve, and a distance larger than 20 Å can be determined in the absence of decay within the 250 ms of CODEX.

Article Title: Understanding Surface and Interfacial Chemistry in Functional Nanomaterials via Solid-State NMR.
Article Snippet: Dr. A. Marchetti, Dr. J. Chen, Z. Pang, Prof. X. Kong Center for Chemistry of High-Performance & Novel Materials Department of Chemistry Zhejiang University Hangzhou 310027, P. R. China E-mail: kxq@zju.edu.cn Dr. S. Li, Dr. F. Deng State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics National Center for Magnetic Resonance in Wuhan Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071, P. R. China E-mail: dengf@wipm.ac.cn Dr. D. Ling Institute of Pharmaceutics College of Pharmaceutical Sciences Zhejiang University 866 Yuhangtang Road, Hangzhou 310058, P. R. China. R ev iew © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim wileyonlinelibrary.com (1 of 38) 1605895 Understanding Surface and Interfacial Chemistry in Functional Nanomaterials via Solid-State NMR Alessandro Marchetti, Juner Chen, Zhenfeng Pang, Shenhui Li, Daishun Ling, Feng Deng,* and Xueqian Kong* Dr. A. Marchetti, Dr. J. Chen, Z. Pang, Prof. X. Kong Center for Chemistry of High-Performance & Novel Materials Department of Chemistry Zhejiang University Hangzhou 310027, P. R. China E-mail: kxq@zju.edu.cn Dr. S. Li, Dr. F. Deng State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics National Center for Magnetic Resonance in Wuhan Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071, P. R. China E-mail: dengf@wipm.ac.cn Dr. D. Ling Institute of Pharmaceutics College of Pharmaceutical Sciences Zhejiang University 866 Yuhangtang Road, Hangzhou 310058, P. R. China DOI: 10.1002/adma.201605895 Today’s chemists heavily rely on many advanced characterization techniques such as optical, X-ray, and electron microscopy, and various types of spectroscopy, to piece together the pictures of the microscopic world.. [19] Among these techniques, solid-state nuclear magnetic resonance (SSNMR) has a remarkable strength and it is an ideal tool for probing short-range ordering and dynamics (Figure 1).

Article Title: Trichogin GA IV Alignment and Oligomerization in Phospholipid Bilayers
Article Snippet: Notably, for a predominantly tetrameric arrangement the statistical probability to also have inter-oligomeric contacts between tetramers affecting the CODEX decay curve is rather small and can be ignored (see SI of reference 18).

Article Title: Effects of Chemical Modification on the Molecular Dynamics of Complex Polyrotaxanes Investigated by Solid-State NMR
Article Snippet: The chemical modification of the pendant hydroxyl functional groups on cyclodextrins (CDs) significantly suppresses the hydrogen-bonding interactions between the cyclodextrin molecules and leads to the unique viscoelastic properties of hydroxypropylated polyrotaxane (HyPR) [Inomata et al. Macromolecules 2010, 43, 4660−4666].. HyPR consists of poly(ethylene glycol) (PEG) and α-CDs that are partially modified with a hydroxypropyl (Hy) group, setting them apart from other polyrotaxanes (PRs).. The molecular dynamics of PR and HyPR with 25% (HyPR25) and 78% (HyPR78) modification ratios were investigated using various solid-state NMR techniques.

Article Title: Characterization of the Slow Molecular Dynamics of Poly( l ‐Lactic Acid) in α and α′ Phases, in a Glassy State, and in a Complex with Poly( d ‐Lactic Acid) by Solid‐State NMR
Article Snippet: [35] The evolution-time dependence of the CODEX decay curve revealed that PLLA chains in the SC and α′ in addition to the α form[34] exhibit large-amplitude helical jump motions, similar to those previously observed for several polyolefins[4–7,9,14] and other polymers.

Activation Assay:

Article Title: Helical jump motions of poly(L-lactic acid) chains in the α phase as revealed by solid-state NMR.
Article Snippet: The molecular dynamics of Poly(L-lactic Acid) (PLLA) chains in the α phase was investigated by Solid-State NMR spectroscopy.. C highresolution NMR clearly indicates that the crystalline signals split into 2, 3, and 4 signals for the CH3, CH and CO groups, respectively at 25 °C, while the amorphous signals give a broad component at the bottom of the crystalline signals.. C NMR spectra show that the crystalline line shape changes with increasing temperatures well above the glass transition temperature (Tg) and imply the presence of the molecular dynamics in the crystalline region.

Image Search Results

Journal: bioRxiv

Article Title: Mechanism of sensor kinase CitA transmembrane signaling

doi: 10.1101/2023.02.06.527302

Figure Lengend Snippet: At the mixing time of 250 ms, the bound state CODEX signal decays to 0.65 of the reference experiment (A, inset yellow); the decay rate fits to an inter-CF 3 distance of 13.6 ±3.0 Å, with the exponential decay fit curve of 0.5 * e −0.0053*t −0.5, matching the expected inter-dimer distance at the C-terminus of the parallel dimer (C). In contrast, the free state CODEX signal is almost the same as the reference experiment (A, inset blue) through all mixing times, corresponding to a large inter dimer distance at the C-terminus of more than 20 Å, agreeing with the anti-parallel dimer (B). Example CODEX decay curves at different inter fluorine distances are shown (A, grey). 30% of the bound state CitApc protein present in the citrate free sample caused the minor CODEX decay. The CODEX decay curve could be acquired beyond the 19 F T 1 of 321ms (Figure S10), thanks to an eight-fold DNP signal enhancement (Figure S9B).

Article Snippet: An inter-CF 3 group distance shorter than about 20 Å is measurable by fitting the CODEX decay curve, and a distance larger than 20 Å can be determined in the absence of decay within the 250 ms of CODEX.

Techniques:

19 F CODEX of 4- 19 F-Phe23-labeled ETM in different lipid membranes at various peptide to phospholipid ratios (P:L). Filled circles are the measured CODEX S/S 0 values, while open circles are the intensity decays of the control spectra S 0 , normalized to the 100 ms spectral intensity. Solid lines are the best-fit matrix simulations of the CODEX decay using an isolated symmetric oligomer model. Dashed lines are the best exponential fit to the S 0 decay to give the 19 F T 1 relaxation time. (a–c) CODEX decays of the ERGIC-bound ETM at varying P:L ratios. (a) P:L = 1:17. (b) P:L = 1:34. (c) P:L = 1:8.5. The best-fit curves use a symmetric pentamer model. (d–f) CODEX intensities shown as inverse S 0 /S ratios for the same three samples as in (a–c), to better compare the pentamer and hexamer fits to the measured data at long mixing times. The best-fit simulations for a symmetric pentamer model (black) and a symmetric hexamer model (purple) are shown in (d) and (f). (g) CODEX decay of the ETM bound to a cholesterol-depleted ERGIC membrane (POPC/POPE/PI/POPS) at P:L = 1:17. (h) CODEX decay of the major Phe23 peak in POPC/POPE/POPS membrane-bound ETM at a P:L of 1:17. The S 0 decays of the major peak (blue open circles) and minor peak (orange open circles) indicate distinct T 1 relaxation times. (i) CODEX decay of the DMPC/DMPG-bound ETM at a P:L ratio of 1:30. The 19 F T 1 times are longer than 3 s in all membranes except for the major peak of the POPC/POPE/POPS-bound sample and the DMPC/DMPG-bound ETM.

Journal: Biochemistry

Article Title: SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers

doi: 10.1021/acs.biochem.2c00464

Figure Lengend Snippet: 19 F CODEX of 4- 19 F-Phe23-labeled ETM in different lipid membranes at various peptide to phospholipid ratios (P:L). Filled circles are the measured CODEX S/S 0 values, while open circles are the intensity decays of the control spectra S 0 , normalized to the 100 ms spectral intensity. Solid lines are the best-fit matrix simulations of the CODEX decay using an isolated symmetric oligomer model. Dashed lines are the best exponential fit to the S 0 decay to give the 19 F T 1 relaxation time. (a–c) CODEX decays of the ERGIC-bound ETM at varying P:L ratios. (a) P:L = 1:17. (b) P:L = 1:34. (c) P:L = 1:8.5. The best-fit curves use a symmetric pentamer model. (d–f) CODEX intensities shown as inverse S 0 /S ratios for the same three samples as in (a–c), to better compare the pentamer and hexamer fits to the measured data at long mixing times. The best-fit simulations for a symmetric pentamer model (black) and a symmetric hexamer model (purple) are shown in (d) and (f). (g) CODEX decay of the ETM bound to a cholesterol-depleted ERGIC membrane (POPC/POPE/PI/POPS) at P:L = 1:17. (h) CODEX decay of the major Phe23 peak in POPC/POPE/POPS membrane-bound ETM at a P:L of 1:17. The S 0 decays of the major peak (blue open circles) and minor peak (orange open circles) indicate distinct T 1 relaxation times. (i) CODEX decay of the DMPC/DMPG-bound ETM at a P:L ratio of 1:30. The 19 F T 1 times are longer than 3 s in all membranes except for the major peak of the POPC/POPE/POPS-bound sample and the DMPC/DMPG-bound ETM.

Article Snippet: Simulation of the 19 F CODEX decay curves yielded nearest-neighbor intrapentamer distances of 8–9 Å for the 4- 19 F-Phe23 labels.

Techniques: Labeling, Isolation

Alternative ETM oligomerization models and their corresponding CODEX simulations. The experimental data (filled circles) are those of ERGIC-bound 4- 19 F-Phe23-labeled ETM at P:L = 1:17. Simulated CODEX decays are shown in solid lines. (a) Measured CODEX decays together with best-fit simulation using an isolated symmetric pentamer model. The simulation is the same as in Figure a. The nearest-neighbor distance of the best-fit pentamer is 8.8 Å. While the overall agreement between the experiment and simulation is good (χ 2 ν = 1.01), the intensities deviate at intermediate (1–2 s) and long mixing times (4 s). (b) Simulated RSA distribution of pentamers in a 100 × 100 nm 2 square. All couplings stronger than 0.85 Hz (50 Å) are considered in the calculation, though convergence occurs around 15 Å. (c) Simulated cluster distribution of pentamers based on a cylinder–cylinder interaction and hydrophobic mismatch model. (d) Measured CODEX decays shown as S/S 0 and the inverse S 0 /S values. These are overlaid with simulated curves for the isolated symmetric pentamer model, the random distribution model, and the clustered distribution model. The clustered pentamer model agrees best with the measured CODEX intensities at long mixing times. (e) Average nearest-neighbor distances from the RSA simulation (blue) and the cluster simulation (red). The distances from the RSA distribution were obtained from 1000 independent simulations. The distances from the interaction potential simulation were obtained from 50,000 Monte Carlo steps to reach a final distribution. (f) Experimental CODEX data with best-fit simulation using an isolated asymmetric pentamer model. Gradient decent fitting yielded better agreement between the experiment and simulations compared to (a), and the nearest-neighbor distances in the model range from 6.5 to 10.4 Å.

Journal: Biochemistry

Article Title: SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers

doi: 10.1021/acs.biochem.2c00464

Figure Lengend Snippet: Alternative ETM oligomerization models and their corresponding CODEX simulations. The experimental data (filled circles) are those of ERGIC-bound 4- 19 F-Phe23-labeled ETM at P:L = 1:17. Simulated CODEX decays are shown in solid lines. (a) Measured CODEX decays together with best-fit simulation using an isolated symmetric pentamer model. The simulation is the same as in Figure a. The nearest-neighbor distance of the best-fit pentamer is 8.8 Å. While the overall agreement between the experiment and simulation is good (χ 2 ν = 1.01), the intensities deviate at intermediate (1–2 s) and long mixing times (4 s). (b) Simulated RSA distribution of pentamers in a 100 × 100 nm 2 square. All couplings stronger than 0.85 Hz (50 Å) are considered in the calculation, though convergence occurs around 15 Å. (c) Simulated cluster distribution of pentamers based on a cylinder–cylinder interaction and hydrophobic mismatch model. (d) Measured CODEX decays shown as S/S 0 and the inverse S 0 /S values. These are overlaid with simulated curves for the isolated symmetric pentamer model, the random distribution model, and the clustered distribution model. The clustered pentamer model agrees best with the measured CODEX intensities at long mixing times. (e) Average nearest-neighbor distances from the RSA simulation (blue) and the cluster simulation (red). The distances from the RSA distribution were obtained from 1000 independent simulations. The distances from the interaction potential simulation were obtained from 50,000 Monte Carlo steps to reach a final distribution. (f) Experimental CODEX data with best-fit simulation using an isolated asymmetric pentamer model. Gradient decent fitting yielded better agreement between the experiment and simulations compared to (a), and the nearest-neighbor distances in the model range from 6.5 to 10.4 Å.

Article Snippet: Simulation of the 19 F CODEX decay curves yielded nearest-neighbor intrapentamer distances of 8–9 Å for the 4- 19 F-Phe23 labels.

Techniques: Labeling, Isolation

a 13 C CP MAS spectra of the exchange S ex (red) and reference signal S 0 (black) for three different mixing times at two temperatures. The resonances are deconvoluted into the amorphous (green) and crystalline exchange (orange) and reference (grey) peak. b CODEX t mix decay curves for four different temperatures resulting in the Arrhenius temperature dependence shown in Figure c.

Journal: Nature Communications

Article Title: Competition between crystal growth and intracrystalline chain diffusion determines the lamellar thickness in semicrystalline polymers

doi: 10.1038/s41467-021-27752-0

Figure Lengend Snippet: a 13 C CP MAS spectra of the exchange S ex (red) and reference signal S 0 (black) for three different mixing times at two temperatures. The resonances are deconvoluted into the amorphous (green) and crystalline exchange (orange) and reference (grey) peak. b CODEX t mix decay curves for four different temperatures resulting in the Arrhenius temperature dependence shown in Figure c.

Article Snippet: The resonances are deconvoluted into the amorphous (green) and crystalline exchange (orange) and reference (grey) peak. b CODEX t mix decay curves for four different temperatures resulting in the Arrhenius temperature dependence shown in Figure c.