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

• Published in: Polymer (Guilford) Vol. 48; no. 10; pp. 3013 - 3020
• Main Authors: Zhang, Linxi, Sun, Tingting, Cheng, Jun, Ma, Haizhu
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 04-05-2007; Elsevier
• Subjects: Aminoacids, peptides. Hormones. Neuropeptides; Analytical, structural and metabolic biochemistry; Applied sciences; Biological and medical sciences; Exact sciences and technology; Force-extension profiles; Fundamental and applied biological sciences. Psychology; LNB sequence; Natural polymers; Physicochemistry of polymers; Proteins; Steered molecular dynamics (SMD); LNB sequence; Force-extension profiles; Steered molecular dynamics (SMD); Peptides; Computer simulation; Stress strain relation; Molecular dynamics method; Chain elongation; Theoretical study; Adsorbed state; Property structure relationship; Microstructure; Aminoacid sequence
• ISSN: 0032-3861; 1873-2291
• DOI: 10.1016/j.polymer.2007.03.046

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.