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This paper presents and tests a method for determining the set of inverse-power coefficients defining the long-range potential tail of a given molecular state by least-squares fitting directly to the energies and inertial rotational constants (Bv ’s) of vibrational levels lying very near dissociation. This approach is superior to the widely used procedure of determining potential points by some inversion procedure and fitting them to the inverse-power form, in that the fit is directly sensitive to the uncertainties in the experimental quantities, and that the parameter uncertainties due to interparameter correlation are greatly reduced. Moreover, the new method gives direct estimates of the number, energies, and other properties of unobserved levels lying above those being fitted. Improved results, including potential parameters up to C10, are presented for the B(3Π+0u) state of I2. [ABSTRACT FROM AUTHOR]

Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed for the first time in atomistic detail that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety. [ABSTRACT FROM AUTHOR]

G-protein-coupled receptors (GPCRs) are membrane proteins with critical functions in cellular signal transduction, representing a primary class of drug targets. Acting by direct binding, many drugs modulate GPCR activity and influence the signaling pathways associated with numerous diseases. However, complete details of ligand-dependent GPCR activation/deactivation are difficult to obtain from experiments. Therefore, it remains unclear how ligands modulate a GPCR's activity. To elucidate the ligand-dependent activation/deactivation mechanism of the human adenosine A2A receptor (AA2AR), a member of the class A GPCRs, we performed large-scale unbiased molecular dynamics and metadynamics simulations of the receptor embedded in a membrane. At the atomic level, we have observed distinct structural states that resemble the active and inactive states. In particular, we noted key structural elements changing in a highly concerted fashion during the conformational transitions, including six conformational states of a tryptophan (Trp2466.48). Our findings agree with a previously proposed view that, during activation, this tryptophan residue undergoes a rotameric transition that may be coupled to a series of coherent conformational changes, resulting in the opening of the G-protein binding site. Further, metadynamics simulations provide quantitative evidence for this mechanism, suggesting how ligand binding shifts the equilibrium between the active and inactive states. Our analysis also proposes that a few specific residues are associated with agonism/antagonism, affinity, and selectivity, and suggests that the ligand-binding pocket can be thought of as having three distinct regions, providing dynamic features for structure-based design. Additional simulations with AA2AR bound to a novel ligand are consistent with our proposed mechanism. Generally, our study provides insights into the ligand-dependent AA2AR activation/deactivation in addition to what has been found in crystal structures. These results should aid in the discovery of more effective and selective GPCR ligands. [ABSTRACT FROM AUTHOR]

Summary: The function of G-protein-coupled receptors is tightly modulated by the lipid environment. Long-timescale molecular dynamics simulations (totaling ∼3 μs) of the A2A receptor in cholesterol-free bilayers, with and without the antagonist ZM241385 bound, demonstrate the instability of helix II in the apo receptor in cholesterol-poor membrane regions. We directly observe that the effect of cholesterol binding is to stabilize helix II against a buckling-type deformation, perhaps rationalizing the observation that the A2A receptor couples to G protein only in the presence of cholesterol (). The results suggest a mechanism by which the A2A receptor may function as a coincidence detector, activating only in the presence of both cholesterol and agonist. We also observed a previously hypothesized conformation of the tryptophan “rotameric switch” on helix VI in which a phenylalanine on helix V positions the tryptophan out of the ligand binding pocket. [Copyright &y& Elsevier]

• The OPLS3e force field for carbohydrates can reproduce experimental structural properties for amylose molecules. • Metadynamics calculations can be used to create torsional free energy maps. • Amorphous starch models can be used to predict moisture uptake. • Activation energies of water in starch agrees quantitatively with experiment. • Glass transition temperatures depression from H 2 O content matches experimental trends. Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (T g) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry T g for amorphous starch, a value which no experimental value is available. [ABSTRACT FROM AUTHOR]