Post-translational modifications inducing protein motifs structural changes in patients with kidney cancer
The present data set covers peak lists (in a universal MGF format) of mass spectrometry data obtained from patients with renal cancer with stages I–IV (n=45, aged 56.7±9.8 years). Peak lists can be used for the data re-analysis with various search engine platforms to identify previously non-reported non-canonical PTMs found in serum samples of studied subjects. In addition, this data set contains excel datasheets with essential information on protein and peptides identification and accompanied meta-data (error, sequence coverage, fragments, scores, confident score, etc.) for each subject. The folder "Results-20210912T111630Z-001" contains serach result files in *.xlsx format; The folder "MGF_data" contains peak list files converted by the MS Converter (Proteowizard, version 3.0.203 64-bit) from the Q-Exactive HF (Thermo) RAW data.
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Mass Spectrometry Protein Registration Mass spectrometry analysis was conducted on a high-resolution Q Exactive-HF mass spectrometer equipped with a nanospray ionization source. The selection of mass spectrometry parameters for data acquisition met the requirement of the Human Proteome Organization (HUPO Guidelines version 3.0) for the minimal length of the detected peptide for consideration and justification of PE1 proteins. Data acquisition was performed in a positive ionization mode in the range of 420–1250 m/z for precursor ions (with resolution R = 60 K) and in a range with the first recorded mass of 110 m/z for fragment ions (with a resolution of R = 15 K). Precursor ions were accumulated for a maximum integration time of 15 ms, and fragment ions were accumulated for a maximum integration time of 85 ms. The top 20 precursor ions with a charge state between z = 2 + and z = 4+ were collected and triggered for fragmentation in high-energy collision dissociation mode with collision energy normalized at 27% and ±20% ramping. Molecular dynamics simulations From the obtained dataset, all the motifs with peptides under consideration were selected if the number of individual blocks of the protein molecule included motifs, where the first and last helices were in contact (d≤14Å). The secondary structure of proteins was determined by the DSSP method by Kabsch and Sander. We investigated the change of certain geometry characteristics for PTM-containing structures associated with kidney cancer development, i.e., the interplanar d and minimum r distance between the helices, the angles θ and φ between the axis of helices, the area S and the perimeter P of the intersection polygon helices projection. The expected value of these quantities was calculated before the start of the experiment, and during the experiment, these values were recorded in a time-dependent manner. Protein subunits with lengths less than 200 amino acid residues were selected for the MD simulation. The long (100 ns) MD simulation experiments were carried out using the GROMACS package, version 2020.4], with a modified GROMOS 54A7 force field, a 2 fs integration time step, and imposed 3D periodic boundary conditions. A 12 Å spherical cut-off function was used to truncate the van der Waals interactions. Electrostatic effects were treated using the particle-mesh Ewald summation  (real space cutoff of 12 Å). The temperature and pressure of the systems were maintained by the V-rescale coupling method at 311 K and the Berendsen coupling method at 1 bar. MD simulations were performed using a simple point-charge (SPC) water model. A certain number of solvent molecules were replaced by Na+ or Cl− ions to make each system electrically neutral. Prior to the MD simulation, all systems were subjected to energy minimization (1,000 conjugate gradient steps) and subsequently heated to 311 K within 0.2 ns. The protein and solvent molecules were separately coupled.