Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field

Coarse-grained (CG) level molecular dynamics simulations are routinely used to study various biomolecular processes. The Martini force field is currently the most widely adopted parameter set for such simulations. The functional form of this and several other CG force fields enforces secondary protein structure support by employing a variety of harmonic potentials or restraints that favor the protein’s native conformation. We propose a straightforward method to calculate the energetic consequences of transitions between predefined conformational states in systems in which multiple factors can affect protein conformational equilibria. This method is designed for use within the Martini force field and involves imposing conformational transitions by linking a Martini-inherent elastic network to the coupling parameter λ. We demonstrate the applicability of our method using the example of five biomolecular systems that undergo experimentally characterized conformational transitions between well-defined structures (Staphylococcal nuclease, C-terminal segment of surfactant protein B, LAH4 peptide, and β2-adrenergic receptor) as well as between folded and unfolded states (GCN4 leucine zipper protein). The results show that the relative free energy changes associated with protein conformational transitions, which are affected by various factors, such as pH, mutations, solvent, and lipid membrane composition, are correctly reproduced. The proposed method may be a valuable tool for understanding how different conditions and modifications affect conformational equilibria in proteins

Influence of Selective Extraction/Isolation of Heme/Hemoglobin with Hydrophobic Imidazolium Ionic Liquids on the Precision and Accuracy of Cotinine ELISA Test

In this study, ionic liquids were used for the selective extraction/isolation of hemoglobin from human serum for cotinine determination using the ELISA Kit. The suitability of hydrophobic imidazolium-based ionic liquids was tested, of which OMIM BF4 (1-methyl-3-octylimidazolium tetrafluoroborate) turned out to be the most suitable for direct extraction of hemoglobin into an ionic liquid without the use of any additional reagent at one extraction step. Hemoglobin was separated quantitatively (95% recovery) from the remaining types of proteins remaining in the aqueous phase. Quantum mechanical calculations showed that the interaction of the iron atom in the heme group and the nitrogen atom of the ionic liquid cation is responsible for the transfer of hemoglobin whereas molecular dynamics simulations demonstrated that the non-covalent interactions between heme and solvent are more favorable in the case of OMIM BF4 in comparison to water. The opposite trend was found for cotinine. Selective isolation of the heme/hemoglobin improved the ELISA test’s accuracy, depending on the cotinine level, from 15% to 30%