Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective variables has proven challenging. Here we suggest that the NMR $S^2$ order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between $S^2$ and entropy. Using the $S^2$ order parameter and a surrogate for the protein enthalpy in conjunction with Metadynamics or Variationally Enhanced Sampling we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. From a more conceptual point of view this implies describing folding as a resulting from a trade off between entropy and enthalpy. We also use $S^2$ in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.
Resonant Coupling Between Electromagnetic Waves and Protein Conformational Dynamics Revealed by Molecular Dynamics Simulations
The College of Medical Technology, Shanghai University of Medicine & Health Sciences（上海健康医学院医学技术学院）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）
Hamming distance geometry of a protein conformational space. Application to the clustering of a 4 ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment
Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide
The Wolfson Department of Chemical Engineering, Technion – Israel Institute of Technology（以色列理工学院沃尔森化学工程系）；Faculty of Mathematics, Technion – Israel Institute of Technology（以色列理工学院数学学院）
