Protein-related items

gmx dssp, gmx rama, gmx wheel

To analyze structural changes of a protein, you can calculate the radius of gyration or the minimum residue distances over time (see sec. Radius of gyration and distances), or calculate the RMSD (sec. Root mean square deviations in structure).

To analyze the secondary structure of a protein (not only for static structures, but also for trajectories), you can use the program gmx dssp, which is a native implementation of DSSP algorithm 176, but also is based on the (DSSP V.4 algorithm) with some additional features. For example, you can take into account native hydrogens from the structure (-hmode gromacs, set by default), while in the original algorithm, hydrogen atoms are set as pseudo-atoms with coordinates based on the coordinates of the MainChain atoms (-hmode dssp). Also, it is possible to conduct a fast search for neighboring residues using Neighbor Search (-nb, default), instead of the slow enumeration of protein residues among themselves according to the “each with each” principle implemented in the original algorithm (-nonb).

One other important analysis of proteins is the so-called Ramachandran plot. This is the projection of the structure on the two dihedral angles \(\phi\) and \(\psi\) of the protein backbone, see Fig. 60:

Fig. 60 Definition of the dihedral angles \(\phi\) and \(\psi\) of the protein backbone.

To evaluate this Ramachandran plot you can use the program gmx rama. A typical output is given in Fig. 61.

Fig. 61 Ramachandran plot of a small protein.

When studying \(\alpha\)-helices it is useful to have a helical wheel projection of your peptide, to see whether a peptide is amphipathic. This can be done using the gmx wheel program. Two examples are plotted in Fig. 62.

Fig. 62 Helical wheel projection of the N-terminal helix of HPr.