Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.     

SNARE derived peptide mimic inducing membrane fusion

SNARE proteins mediate membrane fusion between synaptic vesicles and the plasma membrane. A minimized peptide SNARE model system with reduced complexity was introduced combining the native SNARE transmembrane (TMD) and linker domains with artificial coiled-coil forming peptides. Specific membrane fusion initiated by coiled-coil recognition was shown by lipid and content mixing vesicle assays.     

Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP.     

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron–sulfur clusters with 1–4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400–500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P¹⁺/P^N redox potential is nearly the same independently of whether P¹⁺ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E₀ state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E₀–E₄ states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E₄–E₈) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E₀/E₁ couple.     

Controlled Oligomerization of Lewis Acid/Base‐Stabilized Phosphanylalanes

PAls should stick together : The cyclo‐trimer 2 is obtained by H₂ elimination of Lewis acid/base‐stabilized parent compound of the phosphanylalanes 1 . The elimination is controlled by fine tuning the temperature and solvent conditions. A subsequent H₂ elimination produces the ladder compound 3 . Compounds 2 and 3 are the first of a new class of Group 13/15 compounds which show no additionally donor–acceptor bonds within the framework.

     

Temperature quenched DODAB dispersions: fluid and solid state coexistence and complex formation with oppositely charged surfactant

Dilute dispersions of the synthetic bilayer forming double-chained cationic lipid dioctadecyldimethylammonium bromide (DODAB) were investigated. In dispersions sonicated above the chain melting temperature Tm (approximately 45 degrees C) it was found by H NMR that about 50% of the surfactant chains remained fluid when the samples were cooled to room temperature, which is 20 degrees C below Tm. In contrast, there was no sign of a fluid fraction in unsonicated samples at room temperature. The addition of the anionic surfactant sodium dodecyl sulfate (SDS) to DODAB dispersions at room temperature resulted in the formation of an essentially stoichiometric DODA-DS complex with frozen chains, as seen by titration calorimetry and H NMR experiments. For sonicated samples, turbidity experiments demonstrated that, after a fast complexation reaction, the system remains colloidally stable unless the SDS-to-DODAB mixing ratio is too close to unity. H NMR experiments also showed that in the unreacted DODAB the fraction of fluid chains remained close to 50%, indicating either that SDS reacts equally fast with fluid and frozen DODAB or that there is a relaxation of the fluid fraction after the complexation. The melting enthalpy and the melting temperature of the alkyl chains rise gradually as the mixing ratio increases. We observed with cryo-TEM that the fraction of large unilamellar vesicles was significantly larger after addition of SDS. This indicates vesicle fusion. Based on both wide- and small-angle X-ray scattering patterns, the structure of the equimolar SDS-DODAB complex at 25 degress C was proposed to be lamellar.