Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex

The hypothetical scanning molecular dynamics (HSMD) method is used here for calculating the absolute free energy of binding, ΔA(0) of the complex of the protein FKBP12 with the ligand SB2 (also denoted L8) - a system that has been studied previously for comparing the performance of different methods. Our preliminary study suggests that considering long-range electrostatics is imperative even for a hydrophobic ligand such as L8. Therefore the system is modeled by the AMBER force field using Particle Mesh Ewald (PME). HSMD consists of three stages applied to both the ligand-solvent and ligand-protein systems. (1) A small set of system configurations (frames) is extracted from an MD trajectory. (2) The entropy of the ligand in each frame is calculated by a reconstruction procedure. (3) The contribution of water and protein to ΔA(0) is calculated for each frame by gradually increasing the ligand-environment interactions from zero to their full value using thermodynamic integration (TI). Unlike the conventional methods, the structure of the ligand is kept fixed during TI, and HSMD is thus free from the end-point problem encountered with the double annihilation method (DAM); therefore, the need for applying restraints is avoided. Furthermore, unlike the conventional methods, the entropy of the ligand and water is obtained directly as a byproduct of the simulation. In this paper, in addition to the difference in the internal entropies of the ligand in the two environments, we calculate for the first time the external entropy of the ligand, which provides a measure for the size of the active site. We obtain ΔA(0) = -10.7 ±1.0 as compared to the experimental values -10.9 and -10.6 kcal/mol. However, a protein/water system treated by periodic boundary conditions grows significantly with increasing protein size and the computation of ΔA(0) would become expensive by all methods. Therefore, we also apply HSMD to FKBP12-L8 described by the GSBP/SSBP model of Roux's group (implemented in the software CHARMM) where only part of the protein and water around the active site are considered and long-range electrostatic effects are taken into account. For comparison this model was also treated by the double decoupling method (DDM). The two methods have led to comparable results for ΔA(0) which are somewhat lower than the experimental value. The ligand was found to be more confined in the active site described by GSBP/SSBP than by PME where its entropy in solvent is larger than in the active site by 1.7 and by 5.5 kcal/mol, respectively.     

Determination of ultra-trace levels of priority PBDEs in water samples by isotope dilution GC(ECNI)MS using 81Br-labelled standards

A gas chromatography electron capture negative ionization mass spectrometry (GC(ECNI)MS) procedure for the determination of priority polybrominated diphenyl ethers (PBDEs; congeners 28, 47, 99, 100, 153 and 154) in water samples at regulatory EU levels has been developed. The method is based on the use of ⁸¹Br-labelled PBDEs for isotope dilution analysis and the measurement of ⁷⁹Br/⁸¹Br isotope ratios in gas chromatography peaks with the electron capture negative ionization technique. The suitability of this ion source for the precise and accurate measurement of bromine isotope ratios has been demonstrated. The general ECNI-IDMS procedure was evaluated by the analysis of NIST SRM 1947 (Lake Michigan fish tissue) with satisfactory results. For the analysis of water samples, 500 mL of the samples were spiked with the labelled PBDEs and extracted with 10 mL isooctane for 30 min. The extract was evaporated down to ca. 100 μL and injected in the GC(ECNI)MS. Detection limits ranged from 0.014 ⁻¹ to 0.089 pg mL⁻¹ depending on the congener. Recoveries from real water samples, spiked at a level of 0.5 pg mL⁻¹, ranged from 77% to 102%.     

When do the Recession Cones of a Polyhedral Complex Form a Fan?

We study the problem of when the collection of the recession cones of a polyhedral complex also forms a complex. We exhibit an example showing that this is no always the case. We also show that if the support of the given polyhedral complex satisfies a Minkowski–Weyl-type condition, then the answer is positive. As a consequence, we obtain a classification theorem for proper toric schemes over a discrete valuation ring in terms of complete strongly convex rational polyhedral complexes.     

Tunneling currents that increase with molecular elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.     

Relative stability of the open and closed conformations of the active site loop of streptavidin

The eight-residue surface loop, 45-52 (Ser, Ala, Val, Gly, Asn, Ala, Glu, Ser), of the homotetrameric protein streptavidin has a "closed" conformation in the streptavidin-biotin complex, where the corresponding binding affinity is one of the strongest found in nature (ΔG ～ -18 kcal∕mol). However, in most of the crystal structures of apo (unbound) streptavidin, the loop conformation is "open" and typically exhibits partial disorder and high B-factors. Thus, it is plausible to assume that the loop structure is changed from open to closed upon binding of biotin, and the corresponding difference in free energy, ΔF = F(open) - F(closed) in the unbound protein, should therefore be considered in the total absolute free energy of binding. ΔF (which has generally been neglected) is calculated here using our "hypothetical scanning molecular-dynamics" (HSMD) method. We use a protein model in which only the atoms closest to the loop are considered (the "template") and they are fixed in the x-ray coordinates of the free protein; the x-ray conformation of the closed loop is attached to the same (unbound) template and both systems are capped with the same sphere of TIP3P water. Using the force field of the assisted model building with energy refinement (AMBER), we carry out two separate MD simulations (at temperature T = 300 K), starting from the open and closed conformations, where only the atoms of the loop and water are allowed to move (the template-water and template-loop interactions are considered). The absolute F(open) and F(closed) (of loop + water) are calculated from these trajectories, where the loop and water contributions are obtained by HSMD and a thermodynamic integration (TI) process, respectively. The combined HSMD-TI procedure leads to total (loop + water) ΔF = -27.1 ± 2.0 kcal∕mol, where the entropy TΔS constitutes 34% of ΔF, meaning that the effect of S is significant and should not be ignored. Also, ΔS is positive, in accord with the high flexibility of the open loop observed in crystal structures, while the energy ΔE is unexpectedly negative, thus also adding to the stability of the open loop. The loop and the 250 capped water molecules are the largest system studied thus far, which constitutes a test for the efficiency of HSMD-TI; this efficiency and technical issues related to the implementation of the method are also discussed. Finally, the result for ΔF is a prediction that will be considered in the calculation of the absolute free energy of binding of biotin to streptavidin, which constitutes our next project.     

Hetero-Diels-Alder reaction of phosphinyl and phosphonyl nitroso alkenes with conjugated dienes: an aza-Cope rearrangement

Phosphorylated nitroso alkenes react with cyclic dienes such as cyclopentadiene or cyclohexadiene to afford hetero Diels-Alder-type cycloadducts where the nitroso alkene participates as dienophile component and the cyclic olefin acts as the 4π-electron (diene) system. Subsequent aza-Cope rearrangement affords highly functionalized 5,6-dihydro-4H-1,2-oxazines. Conversely, the reaction of TMS-substituted cyclopentadiene (dienophile) with nitroso alkenes as heterodienes leads directly to bicyclic 1,2-oxazines. Theoretical studies are in agreement with the experimental results and with the new aza-Cope rearrangement proposed.     

Quantum States on Harmonic Lattices

We investigate bosonic Gaussian quantum states on an infinite cubic lattice in arbitrary spatial dimensions. We derive general properties of such states as ground states of quadratic Hamiltonians for both critical and non-critical cases. Tight analytic relations between the decay of the interaction and the correlation functions are proven and the dependence of the correlation length on band gap and effective mass is derived. We show that properties of critical ground states depend on the gap of the point-symmetrized rather than on that of the original Hamiltonian. For critical systems with polynomially decaying interactions logarithmic deviations from polynomially decaying correlation functions are found.     

Linear Key Predistribution Schemes

In a key predistribution scheme, some secret information is distributed among a set of users. For a given family of privileged groups, this secret information must enable every user in a privileged group to compute a common key associated with that group. Besides, this common key must remain unknown to some specified coalitions of users outside the privileged group. We present in this paper a new model, based on linear algebraic techniques, for the design of key predistribution schemes that unifies all previous proposals. This new model provides a common mathematical formulation and a better understanding of key predistribution schemes. Two new families of key predistribution schemes that are obtained by using this model are presented. Those families provide, for some specification structures, schemes that have better information rates than the ones given in previous proposals or fit in situations that have not been considered before.