Molecular dynamics of polymers with explicit but frozen hydrogens

Identification, structure, and agonist design of an androgen membrane receptor

Androgens, such as 5α-dihydrotestosterone (5α-DHT), regulate numerous functions by binding to nuclear androgen receptors (ARs) and potential unknown membrane receptors. Here, we report that the androgen 5α-DHT activates membrane receptor GPR133 in muscle cells, thereby increasing intracellular cyclic AMP (cAMP) levels and enhancing muscle strength. Further cryoelectron microscopy (cryo-EM) structural analysis of GPR133-Gs in complex with 5α-DHT or its derivative methenolone (MET) reveals the structural basis for androgen recognition. Notably, the presence of the "Φ(F/L)2.64-F3.40-W6.53" and the "F7.42××N/D7.46" motifs, which recognize the hydrophobic steroid core and polar groups, respectively, are common in adhesion GPCRs (aGPCRs), suggesting that many aGPCRs may recognize different steroid hormones. Finally, we exploited in silico screening methods to identify a small molecule, AP503, which activates GPR133 and separates the beneficial muscle-strengthening effects from side effects mediated by AR. Thus, GPR133 represents an androgen membrane receptor that contributes to normal androgen physiology and has important therapeutic potentials.

Shadow Hamiltonian in classical NVE molecular dynamics simulations involving Coulomb interactions

Microcanonical ensemble (NVE) Molecular Dynamics (MD) computer simulations are performed with negligible energy drift for systems incorporating Coulomb interactions and complex constraint schemes. In principle, such systems can now be simulated in the NVE ensemble for millisecond time scales, with no requirement for system thermostatting. Numerical tools for assessing drift in MD simulations are outlined, and drift rates of 10^-6 K/μs are demonstrated for molten salts, polar liquids, and room temperature ionic liquids. Such drift rates are six orders of magnitude smaller than those typically quoted in the literature. To achieve this, the standard Ewald method is slightly modified so the first four derivatives of the real space terms go smoothly to zero at the truncation distance, r_c. New methods for determining standard Ewald errors and the new perturbation errors introduced by the smoothing procedure are developed and applied, these taking charge correlation effects explicitly into account. The shadow Hamiltonian, E_s, is shown to be the strictly conserved quantity in these systems, and standard errors in the mean of one part in 10¹⁰ are routinely calculated. Expressions for the shadow Hamiltonian are improved over previous work by accounting for O(h⁴) terms, where h is the MD time step. These improvements are demonstrated by means of extreme out-of-equilibrium simulations. Using the new methodology, the very low diffusion coefficients of room temperature 1-hexyl-3-methyl-imidazolium chloride are determined from long NVE trajectories in which the equations of motion are known to be integrated correctly, with negligible drift.

Shadow Hamiltonian in classical NVE molecular dynamics simulations: A path to long time stability

The shadow energy, E_s, is the conserved quantity in microcanonical ensemble (NVE) molecular dynamics simulations carried out with the position Verlet central-difference algorithm. A new methodology for calculating precise and accurate values of E_s is presented. It is shown for the first time that E_s rather than E is constant during structural changes occurring within a supercooled liquid. It is also explained how to prepare and conduct microsecond range bulk-phase NVE simulations with essentially zero energy drift without the need for thermostating. The drift is analyzed with block averaging and new drift functions of the shadow energy. With such minimal drift, extremely small and accurate standard errors in the mean for quantities like E_s, E, and temperature, T, can be obtained. Values of the standard error for E_s of ≈10^-10 in molecule-based reduced units can be routinely achieved for simulations of 10⁸ time steps. This corresponds to a simulation temperature drift of ≈10^-6 K/μs, six orders of magnitude smaller than generally considered to be acceptable for protein simulations. We also show for the first time how these treatments can be extended with no loss of accuracy to polyatomic systems with both flexible degrees of freedom and arbitrary geometric constraints imposed via the SHAKE algorithm. As a bonus, estimates of simulation-average kinetic and total energies from high order velocity expressions can be obtained to a good approximation from 2nd order velocities and the average mean square force (for polyatomics, this refers to per site, including any constraint forces).

Altered inertial response of generic degrees of freedom

A method to alter the inertial response of generic degrees of freedom is presented. A Hamiltonian acts on the inertial response of a set of independent configurational observables by the introduction of a kinetic bias. The method finds its natural application in reducing the spreading of arbitrary modes in a complex system. The resulting compressed spectrum allows a more efficient sampling of configurational space.