Protein secondary structure is the three-dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three-dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds.
For trajectories with a long simulation time, it is recommended to use the -tu ns option when running gmx do_dssp, so that the time unit in the output ss.xpm is ns, and the drawing is better.
In addition, the residues in the gmx do_dssp output file ss.xpm are the residues you choose to analyze, and the number always starts from 1. If you choose not all the residues when analyzing, then the residue number when drawing is the same as. Residue numbers in the original protein file are inconsistent. For this reason, our two-point script has added another option, which can specify the value of the residue number when drawing. For the above example, if the analyzed residue is from 200 Starting from 1, instead of starting from 1, it should be as follows:
For the obtained secondary structure content file ss~count.xvg, in addition to drawing with ordinary dot-line graphs, stacked histograms can also be used to draw. Gnuplot supports stacked histograms, but its abscissa can only be a string, not Supports continuous values. This is a bit hard to use. One solution is to process the data a bit, and then use boxes to draw. The example is as follows:
Both protein and nucleic acid secondary structures can be used to assist in multiple sequence alignments. In addition to simple sequence information, these alignments can be made more accurate by including secondary structure information. This is sometimes less useful in RNA, because base pairing is much more conserved than sequence. The long-distance relationship between proteins whose primary structure does not match can sometimes be discovered through the secondary structure. Studies have shown that, compared with the β chain in natural proteins, the α-helix is more stable, stronger against mutations and can be designed.