DOI: 10.5281/zenodo.16759006
title: Dataset for: A DFT Study on Trimethylamine N-oxide Interactions with Amino Acid Side Chain Models: Probing the Driving Force of Lysozyme Aggregation

description: Description

This dataset contains the raw experimental and computational data supporting the article: "Beyond Preferential Exclusion: Energetically Favourable TMAO Binding to Denatured Polypeptide Fragments Drives Irreversible Aggregation".

The study investigates the molecular mechanism behind the pro-aggregating effect of trimethylamine N-oxide (TMAO) on lysozyme during thermal denaturation. The data is divided into two main parts: experimental results from Differential Scanning Calorimetry (DSC) and logs from quantum-mechanical (DFT) calculations performed with Gaussian 16.

Content and Structure

The dataset is organized into two ZIP archives:



DSC_results.zip: Contains data from the Nano DSC III calorimeter. The archive includes:



Raw data files (CSC.dsc format): The original, complete output files from the instrument for each experimental run. The filenames specify the sample composition and conditions.

A CSV sub-directory: Contains selected scans exported to a plain-text CSV format for easier access and analysis. The naming convention is as follows:



For protein samples, three scans are provided to assess the reversibility of the denaturation process: 



heating_1: The initial heating scan showing the protein denaturation.

cooling_2: The subsequent cooling scan.

heating_3: The second heating scan (rescan) used to check for protein refolding.



For baseline samples (water and TMAO solution), a single representative scan (scan_13) is provided.





G16_logs.zip: Contains the output log files from Gaussian 16 (Rev. C.02) for all DFT calculations. The calculations were performed using the M06-2X functional and the aug-cc-pVTZ basis set, with the SMD continuum solvation model to simulate an aqueous environment at 353.15 K (80°C).


The archive contains directories named after the relevant amino acid or model system. Each directory includes log files for:





Geometry optimization of the isolated model molecule.

Geometry optimization of hydrated complexes (e.g., model+1H2O.log, model+2H2O).

Geometry optimization of complexes with TMAO and its hydrates (e.g., model+(nH2O)+TMAO(mH2O).log).

Corresponding calculations with Basis Set Superposition Error (BSSE) correction using the counterpoise method (files ending in _BSSE.log).



Note on Computational Models

For clarity, the folder names in G16_logs.zip use common amino acid names. However, the actual calculations were performed on simplified, well-defined models to isolate specific interactions, as described in the manuscript. All energies and enthalpies, including ZPE and BSSE corrections, are compiled in the file Pastwa_2025_ZPE_BSSE_Data.pdf. The correspondence between the folder name and the computational model used is as follows:






Folder Name



Computational Model Used





NMA



N-methylacetamide (model of the peptide bond)





Arginine



N-butylguanidinium





Asparagine



Propanamide





Aspartate



Propanoate





Glutamine



Butanamide





Glutamate



Butanoate





Histidine



4-ethylimidazole





Lysine



1-pentylammonium





Serine



Ethanol





Threonine



Propan-2-ol





Tryptophan



3-ethylindole





Tyrosine



4-ethylphenol





 

Acknowledgements

Computations were carried out using the computers of Centre of Informatics Tricity Academic Supercomputer & Network.