A steered molecular dynamics study on peptide sequence prediction from force-extension profiles

Abstract A study of the peptide sequence prediction based on the steered molecular dynamics (SMD) method is presented. Here, 2 22-residue peptide sequences are selected. One is the neutral sequence and the other is the LNB sequence. Force-extension profiles are easily obtained from the steered molecular dynamics simulation. For the N 22 sequence, it is shown that the force curve is of saw-tooth pattern. There are 22 peaks in the curves, and each peak in the curve denotes one residue in the sequence. For the LNB sequence, 3 force curves corresponding to the desorption from 3 different attractive surfaces are shown. The residues L (hydrophilic), N (neutral), and B (hydrophobic) in the sequence can be read easily from the peaks of the curves. End-to-end distance R 2 is also discussed for the 2-peptide sequences. Finally, we calculate adsorbed energy curves during the desorption process, and there are some steps in the curves, which are like the peaks in the force profiles. That is, from those steps in the energy curves, the residue prediction for the peptide sequence can also be done accurately.