Data for: PathMolD-AB: Spatiotemporal Pathways of Protein Folding using Parallel Molecular Dynamics with a Coarse-grained Model

Published: 15 June 2020| Version 1 | DOI: 10.17632/zh8fp5p7rb.1
Leandro Takeshi Hattori, Bruna Pinheiro, Rafael Frigori, César Benítez, Heitor Lopes


Using the PathMolD-AB software, four datasets of protein folding trajectories were produced as case studies. Four proteins were simulated, one artificially created and three real-world proteins with a growing number of amino acids, the detailed as follows: 13FIBO: it has 13 amino acids, and was artificially created by \cite{stillinger1995collective}, by distributing the hydrophobic amino acids according to the Fibonacci sequence. 2GB1 (http://10.2210/pdb2GB1/pdb): this protein is in the group of the G proteins, which exerts signal transduction functions. The dysfunction of this protein is linked to diseases such as schizophrenia in humans; 1PLC (http://10.2210/pdb1PLC/pdb): this protein performs the function of electron transportation, which is related to the process of energy production in the cell. Its functional impairment results in cell death; 5NAZ ( this is a globular structural protein of collagen, and it is related to the Goodpasture's and Alport's syndromes. Link for the Dataset of Spatiotemporal Pathways of Protein Folding:!C5QkHQ6A!Ng2xowc2hVPoHHiSB7ww-w For each protein, a dataset was generated with 1,000 (for 13FIBO, 2GB1 and 1PLC) or 500 (for 5NAZ) different pathways. Due to the length of the last protein, fewer simulations were done. As mentioned before, all simulations start with structures randomly initialized in the 3D space, to achieve a high diversity of pathways, each one leading to the native conformation of the protein. To guarantee a reliable stabilization of the native structure, the maximum number of time-steps (t_{max}) for the simulations of the 13FIBO, 2GB1 and 1PLC proteins were set to 3x 10^6 iterations and 1x 10^8 for the 5NAZ protein. Consequently, for standardizing the number of spatiotemporal states per pathway in each dataset, the step_size for 13FIBO, 2GB1 and 1PLC were 3000, and 8000 for the 5NAZ. For each pathway, 1,000 folding states were recorded.



Applied Sciences, Bioinformatics, Molecular Modeling, Computational Biochemistry, High Performance Computing