Supplementary Material to "Analysis of consensus motions in proteins through molecular dynamics simulations"
Creators: name: Jorda, Luis
Publisher: name: Zenodo
Year: 2023
Subjects: MD
molecular dynamics
essential dynamics analysis
consensus essential dynamics analysis
proteins
allostery
pyruvate kinase
pathogenicity prediction
structural bioinformatics

description: This supplementary material belongs to the PhD Thesis «Analysis of consensus motions in proteins through molecular dynamics simulations» by Luis Jordà (2023), University of Barcelona, Spain.

The purposes of this material are: i) to facilitate reproducibility and further exploration of technical aspects of the methodology employed throughout the thesis, and ii) to enable visual inspection of the collective motions from the study of human erythrocyte pyruvate kinase (PKR).
description: The contents are structured in three main directories (compressed as ZIP folders):



Directory QM_related_files



Contains the relevant files to trace and reproduce the quantum mechanics (QM) calculations of the project. These comprise geometry optimizations, force-constant calculations, and single-point energy calculations with the Gaussian16 software.



Input files (ASCII files with the .com extension). They contain the input structures and the set of parameters and decisions submitted in every type of calculation, including the frozen-atom schemes of the cluster models for the parameterization of metal centers.

Log files (ASCII files with the .log extension). They contain detailed information of every step and stage in the calculations (parameters, processes, decisions, values…).

Printed information from the checkpoint files (ASCII files with the .gjf extension), namely, the molecular structure (charge, multiplicity, coordinates), the basis set, the Molecular Orbitals, and the forces (if force constants were requested to be calculated).





Directory MD_related_files



Subdirectory force_field_custom_entries



Contains text files (ASCII files with the .txt extension) with descriptions of the steps followed to include new custom residue types, atom types and their respective non-bonded terms in the files of the AMBER99SB-ILDN force field included in the native installation of the GROMACS software. The procedure was adapted from the GROMACS online "Short How-To guides", and involves modifying the aminoacids.rtp, atomtypes.atp, and ffnonbonded.itp files of the force field, and the residuetypes.dat file.



Subdirectory MDP_files



Contains the GROMACS MDP files (Molecular Dynamics Parameters; ASCII files with the .mdp extension) that correspond to several of the stages of the MD workflow of this project (Figure 3.2 from the Methods chapter), namely, energy minimizations, incorporation of dissolved ions, and NVT/NPT simulations. The MDP format contains a list of keywords that are used in the framework of GROMACS to set up the different types of simulation that require use of the grompp tool.



Subdirectory simulation_systems



Contains the structure files (ASCII files in PDB format with the .pdb extension) and the GROMACS topology files (ASCII files with the .top and .itp extensions) of all the systems subjected to MD in this project.

In the case of the systems in the apo condition, the files correspond to the configuration after the placement of hydrogen atoms, right before the stage of energy minimization in vacuum.

In the case of the systems in holo conditions, the files correspond to the configuration after the incorporation of the QM-derived metal-center parameters, right before the repetition of the energy minimization in vacuum.

Importantly, this is the location where all the QM-derived atomic charges and bonded parameters of each type of system can be found.





Directory supplementary_videos



Contains the 30 Supplementary Videos (S4.1 to S4.30) both in MP4 and GIF formats (.mp4 and .gif extensions) that enable visualization of the collective motions reported in the Results chapter. Each video is paired with a text file (ASCII file with the .txt extension) that includes a brief description of the type of visualization and references to figures of the Results chapter.
description: On the other hand, the complete set of simulations and standard trajectory analyses have been made publicly available at the online database PKLR from the Molecular Dynamics Data Bank (https://pklr.mddbr.eu), a project funded by the European Union's Horizon Europe programme under grant agreement 101094651.