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Data for the manuscript entitled "Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer complex"

Version 1.0

Mikulska-Ruminska, Karolina, 2025, "Data for the manuscript entitled "Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer complex"", https://doi.org/10.18150/QAGBGW, RepOD, V1

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Description

This repository provides CHARMM-compatible topology (top) and parameter (par) plain-text files (UTF-8) for molecular dynamics simulations of the FtAlkBG monooxygenase. Files can be opened in any text editor and are directly usable with NAMD (free for academic use) and CHARMM.

Contents: Definitions of atom types and partial charges; bonded terms (bonds, angles, dihedrals, impropers); and nonbonded parameters for two metal sites:

Site3 (AlkG): Fe coordinated by four cysteines — top_all27_Site3.inp, par_all27_Site3.inp.

Site1/2 (AlkB): di-iron site coordinated by nine histidines and one glutamate — top_all27_Site1_2.inp, par_all27_Site1_2.inp.

Project context: This dataset supports molecular dynamics studies of the FtAlkBG monooxygenase, which operates through two coordinated catalytic metal centers: a di-iron site in the AlkB domain (here split into Site1 and Site2 in the topology) and an Fe–(Cys)_4 site in the AlkG domain (Site3). The provided TOP/PAR files supply the necessary atom types, partial charges, and bonded/nonbonded parameters to model these centers and their coordination environments. They are intended for integration into NAMD/CHARMM simulations of FtAlkBG and related constructs.

Force field & units: CHARMM27; energies in kcal/mol, distances in Å, angles in degrees.

Software used: NAMD v2.14

Data authors:

  • Karolina Mikulska-Ruminska - created the files 
  • Mehmed Zahid Ertem - provided partial charges and geometry via QM/MM calculations


Funding: Physical Biosciences Program within the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences (grant no KC030402); computational resources at the Center for Functional Nanomaterials, which is a U.S. Department of Energy Office of Science Facility, and the Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory under Contract No. DE-SC0012704, by National Institutes of Health grants R01 GM139297 and R01 DK116780; Polish National Science Centre no. 2022/46/E/ST4/00053.

See README.md for file organization and usage instructions.

Subject
Chemistry; Physics
Keyword

monooxygenase, molecular dynamics, catalytic site coordination, CHARMM force field

Related Publication

Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer complex, Karolina Mikulska-Ruminska, Matthew Licht, Mehmed Z Ertem, John Shanklin, Qun Liu, Ivet Bahar, bioRxiv, 2025.06. 23.661152 https://www.biorxiv.org/content/10.1101/2025.06.23.661152v1.abstract arXiv: bioRxiv, 2025.06. 23.661152

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readme.txt
Plain Text - 1.3 KB - Nov 19, 2025 - 2 Downloads
MD5: 17370a7f8602bc97c4fa18bf1bd88320
License: CC0 Creative Commons Zero 1.0
Dataset documentation
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par_all27_Site1_2.inp
Plain Text - 14.4 KB - Nov 19, 2025 - 1 Download
MD5: c351b8e5ae8792ca190f6cfb7cf0fe51
License: CC BY - Creative Commons Attribution 4.0
The parameter file of the active site is composed of two irons coordinated by nine histidines and one glutamic acid located in the AlkB domain.
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par_all27_Site3.inp
Plain Text - 3.5 KB - Nov 19, 2025 - 1 Download
MD5: 117d86d6c914fe0a54079e15652dc165
License: CC BY - Creative Commons Attribution 4.0
The parameter file of the active site is composed of iron coordinated by four cysteines located in the AlkG domain.
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top_all27_Site1_2.inp
Plain Text - 25.5 KB - Nov 19, 2025 - 1 Download
MD5: aee8a3656098500f2067ae3542d8f6d0
License: CC BY - Creative Commons Attribution 4.0
Topology file of the active site composed of two irons coordinated by nine histidines and one glutamic acid located in the AlkB domain.
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top_all27_Site3.inp
Plain Text - 6.4 KB - Nov 19, 2025 - 1 Download
MD5: a3b17d94e474e86b3aabf12938fe05e8
License: CC BY - Creative Commons Attribution 4.0
Topology file of the active site composed of iron coordinated by four cysteines located in the AlkG domain.
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