MBM Gruppe

Software and Data

Here you can download the material relative to the articles published by MBM group members:

  • Additional files relative to the work from B. Wang et al. (2013). Isopeptide bonds mechanically stabilize spy0128 in bacterial pili. Biophys J (2013)104(9):2051-7.

Isopeptide bonds

The files relative to the work from B. Wang et al. (2013). Isopeptide bonds mechanically stabilize spy0128 in bacterial pili. Biophys J (2013)104(9):2051-7.

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Redox potential of a protein disuflide bond

Predicting the redox potential of a protein disuflide bond is very useful in various fields, from redox biochemistry to protein allostery to covalent ligand binding to cysteines. We explain in great detail, how you can run Molecular Dynamics simulations in Gromacs such that you obtain the disulfide bond redox potential of interest.

Please find all input files for redox potential calculations using fast growth thermodynamic intergration in gromacs here: redox_potential.tar

Very convincing results have been obtained for different thioredoxin like proteins, as shown in this publication:

W. Li, I. B. Baldus, F. Gräter (2015).
Redox potentials of protein disulfide bonds from free-energy calculations.
J. Phys. Chem. B. 119(17):5386-5391 Link

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Tcl procedure to quantify pre-stress in S-S bonds

Here you will find a tcl script that contains a procedure able to calculate the properties of S-S bonds as defined by Schmidt et al. published in „Biochemistry (2006) Vol. 45 pp. 7429-7433.

The script identifies the S-S bonds in any protein considering that these information are supplied in the pdb file loaded in vmd. These information need to comply the format normally used in PDB files to described the presence of disulphide bonds.
This format is the following and examples can be found in any PDB file of proteins containing disulphide bonds:

SSBOND 1 CYS A 3 CYS A 15

* The script calculates the dihedral angles chi1 to chi1-prime (see Schmidt et al. for details) and from those calculates the strain energy of the bond and the class (-RHSpiral,-LH/RH Staples, etc…) to which the bond belongs.

* Two output files are created:

– One file called SS-chis-summary_{PDBFILE}.dat that contains a summary of which atoms have been used to calculate the chi dihedrals, what are the atom indices etc…

– One file called SS-measures_{PDBFILE}.dat, which contains the values of the chi angles and other properties in the following order:

– Frame number. This is the number of the frame. For single PDB files (x-Ray structures) only one frame will be shown (column 1).
– χ1 to χ5 angle values in degrees (column 2:6).
– The strain energy of the bond (in that particular conformation) calculated in kJ/mol using the empirical formula proposed in the above-mentioned paper (column 7).
– The S-S distance in Å (column 8).
– The class of the S-S bond (column 9).

To use the script load vmd with the molecule (and trajectory) that you want to analyse
In the tcl/tk console window source the file typing „source ${SCRIPT}.tcl“
launch the procedure called ss typing ss ${FILE}.pdb that has been loaded when you launched VMD.

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Force distribution analysis (FDA)

Force distribution analysis (FDA) is a method to detect and follow force and stress propagation in proteins, reminiscent of Finite Element Analysis used to engineer macroscopic structures. The method is based on Molecular Dynamics simulations during which we directly calculate forces between each atom pair in a system. The most recent version of FDA is now implemented in GROMACS-4.5.3.

Watch the video about a graphene sheet broken by an AFM tip here!

In a number of projects, FDA also helped to reveal the mechanism of allostery in proteins. More details are given here.

The FDA code can be downloaded from the FDA-GitHub repository

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