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Access this dataset on Dryad

This dataset includes the original electrochemical, computational, and thermodynamic data associated with the corresponding manuscript. The data supports a study that integrates electrochemical surface modification of a literature-reported insulin-binding peptide (IBP), computational peptide modeling, and thermodynamic binding analyses to evaluate the peptide’s binding performance. It is organized to promote reproducibility and facilitate reuse, with files mapped to corresponding figures and tables in the publication.

Electrochemical Data

The electrochemical dataset includes data from cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and enzyme-linked immunosorbent assay (ELISA) experiments. This data was used to evaluate the surface modification of carbon electrodes, peptide immobilization, and insulin-binding interactions on the modified surfaces.

Computational Data

The computational data consists of output PDB files generated from molecular dynamics (MD) simulations of IBP, both in isolation and in complex with insulin. It also includes docking results before and after energy minimization. These files were used to cluster peptide conformations, assess binding interactions, and evaluate structural stability.

Thermodynamic Data

The thermodynamic data includes thermograms and raw data files in .nitc format from isothermal titration calorimetry (ITC) experiments. This data was used to quantify the binding thermodynamics (enthalpy, entropy, and dissociation constants) of IBP binding to insulin to assess the binding affinity and evaluate the thermodynamic feasibility of using the literature-reported IBP in biosensor development.

Description of the Data and File Structure

All data is organized within three zip folders, each corresponding to a specific type of data collected within the study. To ensure broad accessibility, all proprietary files (.sda, .dta, and .nitc) are accompanied by non-proprietary versions (.csv or .txt) of the same data, allowing all users to access and reuse the dataset regardless of software restrictions.

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1. Electrochemical Data - (IBP_Electrochemistry_Data.zip):

This zip folder contains three subfolders, each corresponding to a distinct experiment type. Each file within these subfolders follows a consistent naming convention that includes the experiment date, the electrode surface composition, and the initials of the experimenter. For CV and ELISA experiments, the experiment name is also included. Examples of these naming conventions are provided below by experiment type:

Cyclic Voltammetry (CV) - (IBP-3G-TEV CV Data)

• Data used in Figure 1

Naming Convention:

YYMMDD_surface_procedure_electrode_initials_experiment, where:

• YYMMDD = experiment date
• surface = surface composition (e.g., amine, diazonium, etc.)
• procedure = specific procedure used (e.g., graft = grafting, reduction = reducing salt)
• electrode = type of electrode used (e.g., GC = glassy carbon)
• initials = initials of the person performing the experiment
• experiment = experiment designation (e.g., CV = cyclic voltammetry)
• Example: 220927_aminediazoniummod_graft_GC2_KMA_CV.DTA

Variables Included:
Each CV data file contains the following information:

• Pt: Data point number, starting with point 0 (integer)
• T: Time since the start of the experiment (in seconds)
• Vf: Measured cell voltage (in volts)
• Im: Measured cell current (in amperes)
• Vu: Uncompensated voltage (in volts)
• Sig: Voltage from the signal generator entering the current amplifier (in volts)
• Ach: Voltage measured using the A/D inputs (in volts)
• IERange: Current range used for measurement (integer)
• Over: A code indicating various kinds of error conditions (in bits)
• Temp: Temperature of the cell or instrument (in Celsius)

Electrochemical Impedance Spectroscopy (EIS) - (IBP-3G-TEV EIS Data)

• Data used in Figures 3-5

Naming convention:
YYMMDD_surface_concentration_electrode_initials, where:

• YYMMDD = experiment date
• surface = surface composition (e.g., dia = diazonium, strep = streptavidin, IBP = protein on surface, exp = experimental surface configuration, scram control = scrambled control, strep control = streptavidin control)
• concentration = insulin concentration used during surface exposure
• electrode = type of electrode used (e.g., GC = glassy carbon)
• initials = initials of the person performing the experiment
• Example: 221222_dia_strep_IBP_100_GC5_KMA.DTA

Variables Included:
Each EIS data file contains the following information:

• Pt: Data point number, starting with point 0 (integer)
• T: Time since the start of the experiment (in seconds)
• Vf: Measured cell voltage (in volts)
• Vm: Legacy measured cell voltage (in volts)
• Ach: Voltage measured using the A/D inputs (in volts)
• Over: A code indicating various kinds of error conditions (in bits)
• Temp: Temperature of the cell or instrument (in Celsius)

Enzyme-Linked Immunosorbent Assay (ELISA) - (IBP-3G-TEV ELISA Data)

• Data used in Figure 9

Naming Convention:
YYMMDD experiment peptides initials, where:

• YYMMDD = experiment date
• experiment = experiment designation (e.g., ELISA = enzyme-linked immunosorbent assay)
• peptides = the peptides used for the assay (e.g., IBP, SCRAM)
• initials = initials of the person performing the experiment
• Example: 230410 ELISA IBP SCRAM KMA.sda

Data Included:
The ELISA data file contains the following information:

• Single-wavelength absorbance measurements at 450 nm using a 96-well plate (8×12). Each value in the 8×12 grid represents the endpoint absorbance recorded for an individual well in the plate.

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2. Computational Data (IBP_Computational_Data.zip)

This zip folder contains four main subfolders, each containing PDB structure files generated through different computational procedures, including molecular dynamics (MD) simulations, docking, and energy minimizations. Although the file format is consistent (.pdb), the origin and purpose of the structures vary. Naming conventions for each subfolder are listed below:

1000 IBP Conformations

Files derived from the isolated IBP MD simulation are named with the prefix ibp_conformation_ followed by a numeric index. These represent evenly spaced snapshots taken from the simulation trajectory, starting from 0 and increasing sequentially to 999 (1,000 conformations total).

• Data used in Table 1

Naming Convention:
ibp_conformation_#.pdb, where:

• # = snapshot index from the MD simulation (0–999)
• Example: ibp_conformation_100.pdb

250 Docked IBP Complexes (Before Minimization)

Predicted docked IBP-insulin complexes from ZDOCK's webserver.

• Data used in Figure 7

Naming Convention:
complex.#.pdb, where:

• # = index assigned to each predicted docking pose (0-250)
• Example: complex.100.pdb

250 Docked IBP Complexes (After Minimization)

These structures correspond to the docked complexes in the previous subfolder but have been energy minimized to relieve steric clashes and improve overall structural quality.

Naming Convention:
complex_#.pdb, where:

• # = index assigned to each predicted docking pose (0-250)
• Example: complex_100.pdb

100 ns MD Simulation Snapshots

This folder contains three additional subfolders, each corresponding to a different peptide complex (either an IBP-insulin complex or a control protein-peptide complex) that was subjected to a 100 ns MD simulation. Each subfolder contains 5,000 evenly spaced snapshots, which are used for stability analysis. All files within these subfolders follow the same naming convention:

• Data used in Figure 8

Naming Convention:
snapshot_#.pdb, where:

• # = snapshot index from the MD simulation (0-4999)
• Example: snapshot_100.pdb

Subfolders:

• Model Structure 385 – IBP-Insulin Complex 41 Snapshots
• Model Structure 489 – IBP-Insulin Complex 72 Snapshots
• SH3-Ark1 Control Complex Snapshots

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3. Thermodynamic Data (IBP_ITC_original_data_files.zip)

This zip folder contains four .nitc files containing raw ITC data.

• Data used in Figure 10

Naming convention:
YYYYMMDD protein/peptide buffer.nitc, where:

• YYYYMMDD = experiment date
• protein/peptide = protein/peptide concentrations
• buffer = buffer concentrations
• Example: 20221030 Insulin (2.5 um) and Binding Buffer (20 mM HEPES, 100 mM NaCl, 2 mM EDTA)

Variables Included:
Each thermodynamic data file contains the following information:

• X: injection: Injection number during the titration
• Y: Area Data (µJ): Integrated heat signal for each injection
• Injection Volume (µL): Volume of titrant delivered to the cell for each injection
• Moles (Syringe): Total number of moles of titrant in the syringe at the time of injection
• Moles (Cell): Total number of moles of titrand in the active cell volume before each injection, after correction for volume displacement
• Mole Ratio: Ratio of moles of titrant to moles of titrand in the active cell volume
• Cell Volume (µL): Active volume of the calorimeter sample cell

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Sharing/Accesss Information

This data is not available from any other source and was not created by analysis of any other dataset.

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Code/Software

There is no code or software included in this dataset.