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Determination of Extension Distance of Amino Acid Linker for Photosystem I and Hydrogenase Fusion

Baker Martin
Chemical and Biomolecular Engineering, University of Tennessee

Using the LAMMPS molecular dynamics code1, I have simulated the E subunit of Photosystem I (PsaE) from cyanobacterium Synechocystis PCC 68032 with an attached eight amino acid chain linker, LPETGGGG. The OPLS-aa potential was used to describe the atomic interactions3. The reported extension distance is measured by calculating the distance between the alpha carbons of the first residue in the linker and the first native residue in PsaE. The minimized extension distance is 11.77Å. During the NPT simulation, the system found a minimal extension distance of 7.57Å and the simulation ended with a maximum extension distance of 22.12Å.

The structure shown below is PsaE with the eight amino acid chain linker attached.

Interactive Structure


Color Legend:

  • grey = carbon
  • blue = nitrogen
  • red = oxygen
  • yellow = sulfur

References

[1] S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J Comp Phys, vol. 117, pp. 1-19, 1995.
[2] P. Barth, P. Savarin, B. Gilquin, B. Lagoutte, and F. Ochsenbein, "Solution NMR Structure and Backbone Dynamics of the Psae Subunit of Photosyetm I from Synechocystis Sp. Pcc 6803," Biochemistry, vol. 41, pg. 13902-13914, 2002.
[3] William L. Jorgensen, Jeffry D. Madura, and Carol J. Swenson, "Optimized Intermolecular Potential Functions for Liquid Hydrocarbons," J Am Chem Soc, vol. 106, pp. 6638-6646, 1984.

posted: April 2016.
updated: April 2016.