Data from: Random heteropolymers as enzyme mimics
Data files
Jul 10, 2026 version files 918.99 KB
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Extended_Data_Fig_3.xlsx
16.06 KB
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Extended_Data_Fig_4.xlsx
126.80 KB
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Extended_Data_Fig_5.xlsx
109.80 KB
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Extended_Data_Fig_6.xlsx
24.10 KB
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Figure_1_source_data.xlsx
10.69 KB
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Figure_2_source_data.xlsx
58.22 KB
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Figure_3_source_data.xlsx
218.34 KB
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Figure_4_source_data.xlsx
341.75 KB
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README.md
13.23 KB
Abstract
Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains unknown to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.
Dataset DOI: https://doi.org/10.5061/dryad.ghx3ffc2r
Dataset attribution and Usage
- Usage of the dataset
- This dataset provides files necessary to reproduce most main and extended data figures. Raw data is provided as .xlsx files.
- Please follow Nature policy to use this dataset for reproduction properly.
- Suggested Citations:
- Dataset DOI: https://doi.org/10.5061/dryad.ghx3ffc2r
- Corresponding author: Ting Xu, tingxu@berkeley.edu
Description of the data and file structure
Details for Figure_1_source_data.xlsx
- Description: This file includes the HLB analysis of RHP-P1 and RHP-S1.
- For the sheet "Figure 1d"
- Dimensions: 3 cols
- Variables
- monomer position: the position number of monomer along a RHP chain
- RHP-P1: HLB value of each monomer position in a representative RHP-P1 chain
- RHP-S1: HLB value of each monomer position in a representative RHP-S1 chain
Details for Figure_2_source_data.xlsx
- Description: This file includes the data from neutron scattering experiments, XANES experiments, catalysis results, and MD analysis.
- For the sheet "Figure 2a right"
- Dimensions: 6 cols
- Variables
- Monomer position: the position number of monomer along a RHP chain
- sidechain and backbone combined RMSF: RMSF in Å
- standard deviation of sidechain and backbone combined RMSF: standard deviation in Å
- HLB value: HLB value of each monomer position in a representative RHP chain
- backbone only RMSF: RMSF in Å
- standard deviation of backbone only RMSF: standard deviation in Å
- For the sheet "Figure 2b left"
- Dimensions: 12 cols
- Variables
- Energy (ev): photon energy in XANES measurements
- SPMA(DIW): the measured sample is SPMA in DI water
- Energy (ev): photon energy in XANES measurements
- RHP-P1 (solid): the measured sample is solid-state RHP-P1
- Energy (ev): photon energy in XANES measurements
- RHP-P1 (buffer): the measured sample is RHP-P1 in buffer
- Energy (ev): photon energy in XANES measurements
- RHP-S1 (solid): the measured sample is solid-state RHP-S1
- Energy (ev): photon energy in XANES measurements
- RHP-S1 (buffer): the measured sample is RHP-S1 in buffer
- Energy (ev): photon energy in XANES measurements
- RHP-S1 (DIW): the measured sample is RHP-S1 in DI water
- For the sheet "Figure 2c left"
- Dimensions: 6 rows, every row represents results of a given catalytic system
- Variables
- conversion: conversion of starting materials to product in %
- standard deviation of conversion: from triplicate experiments; in %
- selectivity: isopulegol to menthoglycol product selectivity in %
- standard deviation of selectivity: from triplicate experiments; in %
- For the sheet "Figure 2c right"
- Dimensions: 10 cols, every two cols represent the RMSF values for SPMA side chains of a given RHP chain in solution and in the presence of isopulegol
- Variables (take sequence 3-conformation 1 as an example)
- sequence 3-conformation 1 (in aqueous solution): RMSF of SPMA side chains in aqueous solution; in Å
- sequence 3-conformation 1 (in the presence of isopulegol): RMSF of SPMA side chains in aqueous solution with isopulegol; in Å
- For the sheet "Figure 2c right inset"
- Dimensions: 2 cols
- Variables
- without isopulegol: Distribution of SPMA side chains RMSF in aqueous solution without isopulegol; in Å
- with isopulegol: Distribution of SPMA side chains RMSF in aqueous solution with isopulegol; in Å
- For the sheet "Figure 2d"
- Dimensions: 4 cols
- Variables
- number of contact (MMA): number of contact between MMA and SPMA
- number of contact (EHMA): number of contact between EHMA and SPMA
- number of contact (OEGMA): number of contact between OEGMA and SPMA
- number of contact (SPMA): number of contact between different SPMA
Details for Figure_3_source_data.xlsx
- Description: This file includes the experiment results from SAXS, UV-vis, and EPR experiments.
- For the sheet "Figure 3a"
- Dimensions: 3 cols; each col represents the molar ratio of flanking monomers around NHSMA in a given RHP
- For the sheet "Figure 3b"
- Dimensions: 6 cols
- Variables:
- q: The scattering vector in 1/Å
- RHP-H1: The scattering intensity of RHP-H1
- model (RHP-H1): Fitted scattering intensity of RHP-H1
- q: The scattering vector in 1/Å
- heme-bound RHP-H1: The scattering intensity of heme-bound RHP-H1
- model (heme-bound RHP-H1): Fitted scattering intensity of heme-bound RHP-H1
- For the sheet "Figure 3c"
- Dimensions: 8 cols
- Variables:
- wavelength (nm): wavelength range measured in UV-vis experiments
- hemin: absorbance (A.U.) of hemin in buffer
- wavelength (nm): wavelength range measured in UV-vis experiments
- RHP-H1: absorbance (A.U.) of heme-bound RHP-H1 in buffer
- wavelength (nm): wavelength range measured in UV-vis experiments
- hemin+imidazole: absorbance (A.U.) of hemin with added imidazole ligands in buffer
- wavelength (nm): wavelength range measured in UV-vis experiments
- De novo H10H24 peptide: absorbance (A.U.) of De novo designed H10H24 peptide with hemin in buffer
- For the sheet "Figure 3d"
- Dimensions: 5 cols
- Variables:
- concentration of hemin (um): concentration of hemin added during the titration experiments
- Absorbance: absorbance (A.U.) of hemin in buffer
- standard deviation: standard deviation in triplicate experiments
- concentration of hemin (um): concentration of hemin used to calculate the fitted curve
- fitting curve: Fitted absorbance of hemin in buffer
- For the sheet "Figure 3d inset"
- Dimensions: 21 cols; the first col represents the wavelength range measured in UV-vis titration experiments, each col after the first col represents a UV-vis curve measured after each titration.
- For the sheet "Figure 3e"
- Dimensions: 8 cols; every two cols represent results of a given system
- Variables:
- Gauss: magnetic field strength
- hemin+imidazole: intensity of hemin with added imidazole ligands in EPR measurement
- Gauss: magnetic field strength
- De novo peptide H11A24: intensity of de novo designed peptide H11A24 with hemin in EPR measurement
- Gauss: magnetic field strength
- RHP-H1: intensity of heme-bound RHP-H1 in EPR measurement
- Gauss: magnetic field strength
- De novo peptide H10A24: intensity of de novo designed peptide H10A24 with hemin in EPR measurement
Details for Figure_4_source_data.xlsx
- Description: This file includes results from kinetic analysis, UV-vis experiments, and temperature cycling.
- For the sheet "Figure 4a"
- Dimensions: 13 cols
- Variables
- concentration of CHP (mM)
- RHP-H1: catalytic assay results from heme-bound RHP-H1
- standard deviation of RHP-H1 results: from triplicate experiments
- myoglobin: catalytic assay results from myoglobin
- standard deviation of myoglobin results: from triplicate experiments
- HRP: catalytic assay results using horseradish peroxidase
- standard deviation of HRP results: from triplicate experiments
- concentration of CHP (mM): used for fitting the results from heme-bound RHP-H1
- RHP-H1 (model fitting): fitting results for heme-bound RHP-H1
- concentration of CHP (mM): used for fitting the results from myoglobin
- myoglobin (model fitting): fitting results for myoglobin
- concentration of CHP (mM): used for fitting the results from HRP
- HRP (model fitting): fitting results for HRP
- For the sheet "Figure 4b"
- Dimensions: 22 cols
- Variables:
- wavelength (nm): wavelength range measured in the UV-vis experiments
- col#2-#22: UV-vis absorbance at different time points
- For the sheet "Figure 4c"
- Dimensions: 2 cols
- Variables:
- time (hr): different time points taken during the experiment
- absorbance at 366 nm: UV-vis absorbance at different time points
- For the sheet "Figure 4d left"
- Dimensions: 5 cols
- Variables:
- time (s): different time points taken during the experiment
- RHP-H3: catalytic assay results from heme-bound RHP-H3
- annealed at 40 degree: catalytic assay results from heme-bound RHP-H3 after annealing at 40 degree
- annealed at 60 degree: catalytic assay results from heme-bound RHP-H3 after annealing at 60 degree
- annealed at 80 degree: catalytic assay results from heme-bound RHP-H3 after annealing at 80 degree
- For the sheet "Figure 4d left inset"
- Dimensions: 5 cols
- Variables:
- wavelength (nm): wavelength range measured in the UV-vis experiments
- RHP-H3: UV-vis results from heme-bound RHP-H3
- annealed at 40 degree: UV-vis results from heme-bound RHP-H3 after annealing at 40 degree
- annealed at 60 degree: UV-vis results from heme-bound RHP-H3 after annealing at 60 degree
- annealed at 80 degree: UV-vis results from heme-bound RHP-H3 after annealing at 80 degree
- For the sheet "Figure 4d right"
- Dimensions: 3 cols
- Variables:
- annealing cycle: number of annealing cycle performed on RHP
- activity retention (%): from comparing catalytic assay results before and after annealing
- standard deviation: from triplicate experiments
Details for Extended_Data_Fig_3.xlsx
- Description: This file includes molecular simulation data related with RMSF and surface composition of RHP-S1.
- For the sheet "Extended data Fig 3a"
- dimensions: 3 cols
- variables:
- entry: different monomer
- Backbone RMSF: in Å
- Sidechain RMSF: in Å
- For the sheet "Extended data Fig 3c"
- dimensions: 179 rows, every 17 rows represent the sequence and surface composition by mass for a given RHP sequence
- variables: take sequence 1 as an example
- the first 5 rows show the sequence composition by mass
- the last 11 rows show the surface composition by mass for 10 independent conformation
Details for Extended_Data_Fig_4.xlsx
- Description: This file includes molecular simulation data related with RMSF of backbone and sidechain in RHP-P1.
- For the sheet "Extended data Fig 4a"
- dimensions: 79 cols, every 7 cols represent the results of a given RHP sequence
- variables: take sequence 1 as an example
- Sequence 1 HLB: HLB value of each monomer along the RHP chain
- Sequence 1 backbone+sidechain RMSF: in Å
- Sequence 1 backbone+sidechain RMSF standard deviation: in Å from triplicate experiments
- Sequence 1 backbone RMSF: in Å
- Sequence 1 backbone RMSF standard deviation: in Å from triplicate experiments
- Sequence 1 sidechain RMSF: in Å
- Sequence 1 sidechain RMSF standard deviation: in Å from triplicate experiments
- For the sheet "Extended data Fig 4b"
- dimensions: 4 cols
- variables:
- HLB: HLB value of each monomer along the RHP chain
- backbone + sidechain RMSF: in Å
- backbone RMSF: in Å
- sidechain RMSF: in Å
Details for Extended_Data_Fig_5.xlsx
- Description: This file includes molecular simulation data related with RMSF of backbone and sidechain in RHP-S1.
- For the sheet "Extended data Fig 5a"
- dimensions: 79 cols, every 7 cols represent the results of a given RHP sequence
- variables: take sequence 1 as an example
- Sequence 1 HLB: HLB value of each monomer along the RHP chain
- Sequence 1 backbone+sidechain RMSF: in Å
- Sequence 1 backbone+sidechain RMSF standard deviation: in Å from triplicate experiments
- Sequence 1 backbone RMSF: in Å
- Sequence 1 backbone RMSF standard deviation: in Å from triplicate experiments
- Sequence 1 sidechain RMSF: in Å
- Sequence 1 sidechain RMSF standard deviation: in Å from triplicate experiments
- For the sheet "Extended data Fig 5b"
- dimensions: 4 cols
- variables:
- HLB: HLB value of each monomer along the RHP chain
- backbone + sidechain RMSF: in Å
- backbone RMSF: in Å
- sidechain RMSF: in Å
Details for Extended_Data_Fig_6.xlsx
- Description: This file includes SANS data of RHP-P1 and RHP-S1.
- For the sheet "Left RHP-P1"
- Dimensions: 3 cols
- Variables:
- Q (1/A): The scattering vector in 1/Å
- I (1/cm): The scattering intensity of RHP-P1
- model fitting I (1/cm): Fitted scattering intensity of RHP-P1
- For the sheet "Right RHP-S1"
- Dimensions: 3 cols
- Variables:
- Q (1/A): The scattering vector in 1/Å
- I (1/cm): The scattering intensity of RHP-S1
- model fitting I (1/cm): Fitted scattering intensity of RHP-S1
Code/software
Source codes for metalloprotein surface analysis and sample data are available at GitHub (https://github.com/TingXuGroup/Surface-Anaysis). Source codes for RHP sequence simulation and principal component analysis have been previously published and are available at GitHub (https://github.com/ivanjayapurna/RHPapp and https://github.com/Shunili/AE-RHP, respectively).
