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Updated: Jun 1, 2026
Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
Published on: April 26, 2024
Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using
Shih-Wei Hung1, Pai-Yi Hsiao, Ching-Chang Chieng
1Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
Abstract:
Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.
