Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

“…[9]), incomplete conformational sampling and force-field limitations. Differences between explicit and implicit solvent treatments have been observed with various GB implementations [34,35] and are addressed in more recent GB implementations with improved balance of solvation and intramolecular interactions [36,37].…”

“…These parameters did not have a significant impact on the properties of the Trp7 sidechain, which interacted mostly with the aqueous solvent. In the future, we plan to simulate several compstatin analogs with the CMAP [38,39] and indole [41] modifications of the all-atom C22 force field, and perform a systematic comparison with the results of a recent CMAP/implicit solvent (GB) force field [36,37].…”

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

“…In this model, several atoms in proteins and lipids are approximated as a single united particle and four water molecules are treated as a single particle. Another popular model is the combination of an explicit protein representation with a mean-field solvent/membrane model such as the generalized Born (GB) model where the effects of solvent and membrane are included implicitly in the MD simulations [51,52]. Many MD simulations based on enhanced conformational sampling algorithms have been carried out with the GB models.…”

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations

“…As the interaction takes place in a physiological environment, an accurate model of solvation and hydrophobic interactions is also necessary to evaluate binding energy via a theoretical approach. 18 We have used an energy decomposition protocol to analyze the significant atomic interactions in PA-IIL-monosaccharide interactions. We have employed Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and normal mode analysis to compute free energy of the interactions.…”