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mcmc calculations  (MathWorks Inc)


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    MathWorks Inc mcmc calculations
    a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from <t>MCMC</t> calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.
    Mcmc Calculations, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Detection of phosphorylation post-translational modifications along single peptides with nanopores"

    Article Title: Detection of phosphorylation post-translational modifications along single peptides with nanopores

    Journal: Nature biotechnology

    doi: 10.1038/s41587-023-01839-z

    a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from MCMC calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.
    Figure Legend Snippet: a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from MCMC calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.

    Techniques Used: Polymer, Residue, Phospho-proteomics, Standard Deviation



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    mcmc calculations  (MathWorks Inc)
    90
    MathWorks Inc mcmc calculations
    a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from <t>MCMC</t> calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.
    Mcmc Calculations, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mcmc calculations/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    mcmc calculations - by Bioz Stars, 2026-04
    90/100 stars
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    a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from MCMC calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.

    Journal: Nature biotechnology

    Article Title: Detection of phosphorylation post-translational modifications along single peptides with nanopores

    doi: 10.1038/s41587-023-01839-z

    Figure Lengend Snippet: a, Freely jointed chain (FJC) model of a POC-containing peptide βCAT. Each unit in the polymer has an electrical charge and a typical distance α between residues. Phosphoserine PTMs pS1 and pS2 add a charge of −2 to that unit. b, Electric potential profile (color gradient) in the MspA pore26. The POC was confined within the physical boundaries of MspA (black) and anchored at the Hel308 hold point (pink x). The volumetric map of the MspA cross-section is shown in gray. c, Snapshots of the polymer configuration within MspA from MCMC calculations for the p2βCAT POC at five Hel308 steps. The phosphoserine residue (pS2) (purple) is observed to move through the pore in a nonlinear fashion. Note that the POC polymer gets stretched towards Hel308 step 19, after which the PTM moves into the pore lumen and the polymer relaxes. Orange lines indicate the sensing region of MspA. d, Mean z-location of the pS2 PTM versus Hel308 step number. e, Same for all PTMs in the peptide variants. f, Probability that a pS occupied the sensing region for various βCAT PTM variants versus Hel308 step. g, Experimentally measured ion currents for βCAT phosphopeptide variants where the ion current measured for the non-PTM βCAT was subtracted (from data in Fig. 1g). Shaded error bar is the standard deviation.

    Article Snippet: Simulation methods MCMC calculations 26 were implemented in MATLAB.

    Techniques: Polymer, Residue, Phospho-proteomics, Standard Deviation