Acetylcholinesterase complexed with bivalent ligands related to huperzine a: experimental evidence for species-dependent protein-ligand complementarity

Acetylcholinesterase (AChE) inhibitors improve the cognitive abilities of Alzheimer patients. (-)-Huperzine A [(-)-HupA], an alkaloid isolated from the club moss, Huperzia serrata, is one such inhibitor, but the search for more potent and selective drugs continues. Recently, alkylene-linked dimers of 5-amino-5,6,7,8-tetrahydroquinolinone (hupyridone, 1a), a fragment of HupA, were shown to serve as more potent inhibitors of AChE than (-)-HupA and monomeric 1a. We soaked two such dimers, (S,S)-(-)-bis(10)-hupyridone [(S,S)-(-)-2a] and (S,S)-(-)-bis(12)-hupyridone [(S,S)-(-)-2b] containing, respectively, 10 and 12 methylenes in the spacer, into trigonal TcAChE crystals, and solved the X-ray structures of the resulting complexes using the difference Fourier technique, both to 2.15 A resolution. The structures revealed one HupA-like 1a unit bound to the "anionic" subsite of the active-site, near the bottom of the active-site gorge, adjacent to Trp84, as seen for the TcAChE/(-)-HupA complex, and the second 1a unit near Trp279 in the "peripheral" anionic site at the top of the gorge, both bivalent molecules thus spanning the active-site gorge. The results confirm that the increased affinity of the dimeric HupA analogues for AChE is conferred by binding to the two "anionic" sites of the enzyme. Inhibition data show that (-)-2a binds to TcAChE approximately 6-7- and > 170-fold more tightly than (-)-2b and (-)-HupA, respectively. In contrast, previous data for rat AChE show that (-)-2b binds approximately 3- and approximately 2-fold more tightly than (-)-2a and (-)-HupA, respectively. Structural comparison of TcAChE with rat AChE, as represented by the closely related mouse AChE structure (1maa.pdb), reveals a narrower gorge for rat AChE, a perpendicular alignment of the Tyr337 ring to the gorge axis, and its conformational rigidity, as a result of hydrogen bonding between its hydroxyl group and that of Tyr341, relative to TcAChE Phe330. These structural differences in the active-site gorge explain the switch in inhibitory potency of (-)-2a and 2b and the larger dimer/(-)-HupA potency ratios observed for TcAChE relative to rat AChE. The results offer new insights into factors affecting protein-ligand complementarity within the gorge and should assist the further development of improved AChE inhibitors.     

Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides

Ultraviolet photoelectron spectroscopy in an ion beam was used to investigate the electronic properties of isolated DNA oligonucleotides [dA(5)-4H](4-) and [dT(5)-4H](4-), carrying four excess negative charges. We find the fourth adiabatic electron affinity to be slightly negative for [dA(5)-4H](4-), while it is positive for [dT(5)-4H](4-). This implies a significant influence of the base composition on energetics, which is in turn relevant for analytic applications and also for charge transport properties.     

Design and evaluation of a Dean vortex-based micromixer

A mixer, based on the Dean vortex, is fabricated and tested in an on-chip format. When fluid is directed around a curve under pressure driven flow, the high velocity streams in the center of the channel experience a greater centripetal force and so are deflected outward. This creates a pair of counter-rotating vortices moving fluid toward the inner wall at the top and bottom of the channel and toward the outer wall in the center. For the geometries studied, the vortices were first seen at Reynolds numbers between 1 and 10 and became stronger as the flow velocity is increased. Vortex formation was monitored in channels with depth/width ratios of 0.5, 1.0, and 2.0. The lowest aspect ratio strongly suppressed vortex formation. Increasing the aspect ratio above 1 appeared to provide improved mixing. This design has the advantages of easy fabrication and low surface area.     

Structure and magnetic properties of tetraarylporphinatomagnesium(II) electron transfer salts of 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane,TCNQF4

The crystal structures of the 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, TCNQF(4), electron transfer salts of meso-tetraphenylporphinatomagnesium(II), [MgTPP][TCNQF(4)].PhMe and [MgTPP][TCNQF(4)].3(1,2-C(6)H(4)Cl(2)), and meso-tetrakis(3,4,5-trimethoxyphenyl)porphinatomagnesium(II), [MgT(3,4,5-OMe)PP][TCNQF(4)].3(1,2-C(6)H(4)Cl(2)), provide the first structurally characterized examples of 1-D metal-radical chains involving [Mg(II)(porphyrin(*))](+). These salts possess [TCNQF(4)](*-) stabilized by trans-mu-coordination to Mg(II) and exhibit nu(CN) at 2199 and 2177, 2212 and 2187, and 2194 and 2172 cm(-1), respectively. The [TCNQF(4)](*-) species is planar and bridges two cations with MgN distances of 2.266(16), 2.221(2), and 2.276(3) A, respectively, which are shorter than the MnN 2.321(3) A distance observed for [MnT(3,4,5-OMe)PP][TCNQF(4)].3(1,2-C(6)H(4)Cl(2)). The room-temperature effective moments for [MgTPP][TCNQF(4)].xS (S = PhMe and 1,2-C(6)H(4)Cl(2)) and [MgTPP][C(4)(CN)(6)].PhMe are consistent with the calculated spin only value of 2.45 micro(B) with weak antiferromagnetic coupling (J(intra)/k(B) approximately -2.9 K; H = -2JSa.Sb) for these [TCNQF(4)](*-) salts and for this [C(4)(CN)(6)](*-) salt (J(intra)/k(B) approximately -0.8 K) on the basis of fits to several models. The coupling is significantly reduced with respect to that of the Mn analogues due to lack of spin on the metal site for [Mg(II)(por(*))](+). The antiferromagnetic coupling is enhanced for [MgT(3,4,5-OMe)PP][TCNQF(4)] with respect to [MgTPP][TCNQF(4)] as [TCNQF(4)](*-) gets closer to the [Mg(II)(por(*))](+) plane, which leads to greater interactions and coupling.     

Direct measurement of the radiative lifetime of the A2Σ+(υ′ = 0, K′ = 1, J′ = 32) state of OH and OD

The radiative lifetime of the A²Σ⁺(υ′ = 0, K′ = 1, J′ = 3/2) state of OH and OD has been directly measured by following the decay of fluorescence excited by light from a frequency doubled dye laser. Stern-Volmer extrapolation of the results to zero pressure gave τ(OH) = 788 ± 13 ns and τ(OD) = 754 ± 12 ns.     

On assignment of fundamental vibrational modes of hypophosphite anion and its deuterated analogue

Results of ab initio and density functional theory calculations on the structure and vibrational frequencies of hypophosphite anion indicate earlier experimental assignments of the fundamental vibrational modes are correct while the recent reassignments of several modes proposed by Bickley et al. are inconsistent with the calculated results.     

A simple sum rule for total radiative decay rates in diatomics

The quantity (ν³μ_e²), which occurs in expressions for the total radiative decay rate for an excited vibronic state of a diatomic, is evaluated as a simple expectation value for the initial state. In test calculations this expectation value agrees with the exact sum over states within ≈0.2%.     

How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.     

Paradigms and paradoxes: patterns and estimation of the entropy of formation of aqueous hydrogen containing mono and polynuclear oxyanions

“Simple” energetic patterns, where simple means the use of parameters derived only from the stoichiometry of these species, are relatively rarely discussed in the literature. In addition, entropy studies have been dominated by derivation of the absolute quantity S° rather than the entropy of formation (TΔ_f S ^o). Relationships between the entropy of formation and different parameters such as negative value of the charge of the species, the number of oxygen atoms, the natural logarithm of the molecular weight, the total number of atoms and the number of central atoms that are gases were recently discussed by us for aqueous polynuclear oxyanions. As shown here hydrogen containing anions do not follow this pattern. In this study, new approaches for the estimation of the entropy of formation of aqueous hydrogen containing mono and polynuclear oxyanions are suggested, evaluated and recommended.