Dataset Open Access

Structure and Stability of [4Fe-4S]-Maquettes with Non-coded Amino Acids

Robert Szilagyi

The dataset provides supporting information to a hypothesis of coded Cys being thermodynamically superior to non-coded homoCys and thioGly analogues. The results were first presented at the 30/80 Chemobrionics 2019 meeting in Granada, Spain (www.chemobrionics.eu) and the corresponding publication appears in the thematic issue Frontiers Interface RSC journal.

The data set organized accordingly to the published figures and tables.
Folders starting with numbers correspond to figures in the paper. The force field key files are to be used in combination of the amber99sb.prm force field, as provided by the Tinker 8.7 (dasher.wustl.edu/tinker/).

The full secondary structure analysis was carried out using our in-house code (10.5281/zenodo.1442864).

The folder 'trajectories' contains the peptides without the waterbath, while the 'waterbath' folder has the NPT equilibrated 6 nm waterbath in truncated octahedron geometry.

The files starting with thermodynamics in the top folder has the numerical results used for calculating the cluster stability and ligand exchange reaction energetics.

The folders 'reference cubane' and 'maquette with short peptides' contains the spin-polarized, ferro and antiferro-magnetically coupled electronic structure for all [4Fe-4S] cluster complexes.

The key for the file extensions is as follows:

FCHK: formatted Gaussian16 checkpoint file with spin polarized wave function
KEY: Tinker control keyword file
LOG: output file generated by a computer code
LST: clear text file with the content of a compressed tar archive
MSV: Discovery Studio Viewer Pro 5.0 binary file
MD5: file checksum according to MD5 protocol
ODS: Open Office electronic spreadsheet file
PDW: PsiPlot data file
PDB: Protein Databank Files
PGW: PsiPlot graphics file
PRM: Tinker force field parameter file
TGZ: compressed tar archive
TXT: clear text file or raw data set
TXYZ: Tinker XYZ file with atomic, positions, atom types, and connectivity 
XYZ: Xmol file with atomic positions in Cartesian coordinates
 

Computations were carried out on the Hyalite High Performance Computing System, operated and supported by University Information Technology Research Cyberinfrastructure at Montana State University, Bozeman, MT. This work was supported by the National Science Foundation, Chemistry of Life Processes program, Grant #1609557.
Files (2.7 GB)
Name Size
1 - short peptide initial structures.zip
md5:4c5f8a936a40748de22b7c89076ffd94
64.0 kB Download
2 - short peptide secondary structure.zip
md5:d302c1c7e1419a411971ed831a1199b0
37.2 MB Download
3 - short peptide nests.zip
md5:980336a3708d1a7e9300d46e8cbffa6f
233.7 kB Download
4 - long peptide secondary structure.zip
md5:839cddf6fd38f66c595e58cc7ea655da
35.0 MB Download
5 - reference cubane.zip
md5:0c2aa8fe3af7c44960b9f864a3efc772
165.6 MB Download
6 - maquettes with short peptides.zip
md5:7cb79b1641ed8505bf3c058dcfbe28e1
937.8 MB Download
force field key files.zip
md5:bdac05a30842dab566f2ddf4451ee3cf
33.4 kB Download
README.txt
md5:f7d39ff4bb5208ec4eb29aac793ff9cd
2.0 kB Download
thermodynamics maquettes.ods
md5:109ee1acb7946ddd88d744751af3a3da
35.8 kB Download
thermodynamics reference cubane .ods
md5:3b039012d50d404afbdaf55cb192b85e
56.6 kB Download
trajectories.zip
md5:90a11be132e6d29cbf57f4a05e890f3e
1.6 GB Download
waterbath.zip
md5:55a6c443dacfb2d7a1cc0cde6d7b726d
514.5 kB Download
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