During secondary structure "Number of residues Vs Time" plot, I got these values;
at 300 K: Average number of residues 136.7782
at 325 K: Average number of residues 151.2973
at 350 K: Average number of residues 158.8725
at 375 K: Average number of residues 134.971
at 400 K: Average number of residues 132.994
The average number of residues are maximum in case of 350 K. So??? That means the secondary structural elements are more stable at 350? Or maximum number of residues are maintained at 350 K? I am attaching one sample graph. Please suggest. Thanks
Hi Iqbal,
DSSP program, used to calculate the secondary structure evolution of a protein over time.
In other words, DSSP analysis is used to measure the secondary structure content of a protein as a function of time.
dssp calculate secondary structure for each frame of a trajectory.
The analysis breaks down secondary structure assignments (i.e. helix, sheet, turn, etc.) by individual residues for each time step, allowing you to visualize or quantify the data in meaningful ways.
Hi Mahendra
I know all these definitions you posted above. Read my question first and answer if you can. What is the significance od High/Low numbers of residues/time of same protein at different temperatures? Is it related to Folding?? Stability?? packing??
Thanks
Perhaps these measures refers to the number of residues that forms the secondary structure elements in a certain time. I suggest you to use do_dssp command in gromacs to evaluate the stability during the time of the protein to evaluate the formation of ss element . Sure temperature influence the stability and the folding of protein because high temperature can broken more fast bond between residues and this can be evidenced by your plot in which there is more fluctuation. My advice is to do a do_dssp to understand well what happen during simulation.
Best regards
Andrea Polo.
In my case maximum fluctuations are observed at 375/400 K but the max no of residues forming sec strc is at 350 K. Does it mean that at 350 K protein has max sec str elements i.e maximum fold i.e maximum stable?
I did do-dssp. I prefer to use this graph for analysis.
Protein form ss elements in every time but is not possible to make assumption on stability without almost an hydrogen bond analysis.
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