Alan C. Goren

Understanding Microscopic Binding of Human Microsomal Prostaglandin E Synthase-1 (mPGES-1) Trimer with Substrate PGH2 and Cofactor GSH: Insights from Computational Alanine Scanning and Site-directed Mutagenesis

Microsomal prostaglandin E synthase-1 (mPGES-1) is an essential enzyme involved in a variety of diseases and is the most promising target for the design of next-generation anti-inflammatory drugs. In order to establish a solid structural base, we recently developed a model of mPGES-1 trimer structure by using available crystal structures of both microsomal glutathione transferase-1 (MGST1) and ba3-cytochrome c oxidase as templates. The mPGES-1 trimer model has been used in the present study to examine the detailed binding of mPGES-1 trimer with substrate PGH(2) and cofactor GSH. Results obtained from the computational alanine scanning reveal the contribution of each residue at the protein-ligand interaction interface to the binding affinity, and the computational predictions are supported by the data obtained from the corresponding wet experimental tests. We have also compared our mPGES-1 trimer model with other available 3D models, including an alternative homology model and a low-resolution crystal structure, and found that our mPGES-1 trimer model based on the crystal structures of both MGST1 and ba3-cytochrome c oxidase is more reasonable than the other homology model of mPGES-1 trimer constructed by simply using a low-resolution crystal structure of MGST1 trimer alone as a template. The available low-resolution crystal structure of mPGES-1 trimer represents a closed conformation of the enzyme and thus is not suitable for studying mPGES-1 binding with ligands. Our mPGES-1 trimer model represents a reasonable open conformation of the enzyme and is therefore promising for studying mPGES-1 binding with ligands in future structure-based drug design targeting mPGES-1.

Photoelectron spectroscopy of sulfur atoms produced via two‐photon dissociation of sulfur dioxide

The 2+1 resonantly enhanced multiphoton ionization (REMPI) spectrum of sulfur atoms produced by two‐photon photodissociation of sulfur dioxide is reported for the wavelength range 252–263 nm. Photoelectron spectroscopy of many resonant ionizations reveals a propensity toward preservation of ion core configuration in formation of ionic species. Several pathways for production of pure populations of excited state 2DJo sulfur ions are documented. Photoelectron angular distributions show contributions from outgoing electrons with a maximum angular momentum lmax=2. Intermediate state alignment from two‐photon absorption of ground state 3P0 sulfur atoms is demonstrated.

Ligand field spectroscopy of Cu(II) and Ag(II) complexes in the gas phase: theory and experiment

Ligand field spectra have been recorded in the gas phase for the two series of complexes containing either Cu(II) or Ag(II) in association with pyridine. Where comparisons are possible, the gas phase spectra match those recorded in the condensed phase; however, for Ag(II) systems the results differ in interpretation. The Ag(II) data are attributed to a ligand-to-metal charge transfer process, and the Cu(II) data (spectral region and extinction coefficient) match the characteristics of a d-d transition. A detailed theoretical analysis of two complexes. [Cu(py)4]2+ and [Ag(py)4]2+ provides evidence of a minimum energy, D4h structure and two less stable D2h and D2d structures within approximately 60 kJ mol(-1). From these structures it is possible to identify a range of optically and vibronically allowed transitions that could contribute to spectra observed in the gas phase. In the case of calculations on [Ag(py)4]2+ there is strong evidence of an electronic transition that would account for the observation of charge transfer in the experiments. Less detailed calculations on [Cu(py)6]2+ and [Ag(py)6]2+ show structural evidence of extensive Jahn Teller distortion. Taken together with incremental binding energies calculated for complexes containing between two and six pyridine molecules, these results show that the level of theory adopted is capable of providing a semi-quantitative understanding of the experimental data.

B3LYP calculations on bishomoaromaticity in substituted semibullvalenes

B3LYP/6‐31G* calculations on the degenerate rearrangements of substituted semibullvalenes spuriously predict the relative enthalpies of the bishomoaromatic TSs to be lower than the experimental values. However, the calculations do make the useful and experimentally testable prediction that the two cyano and two phenyl substituents in 2,6‐dicyano‐4,8‐diphenylsemibullvalene (9d) are more likely than four cyano substituents in 2,4,6,8‐tetracyanosemibullvalene (9f) or the four phenyl substituents in 2,4,6,8‐tetraphenylsemibullvalene (9g) to produce a semibullvalene that has a bishomoaromatic equilibrium geometry in the gas phase. The major reason for the surprising finding that 9d is more likely to be bishomoaromatic than 9g is shown to be steric interactions between the phenyl groups at C‐2 and C‐8 and at C‐4 and C‐6 in bishomoaromatic structure 10g. These interactions inhibit the conjugative stabilization of 10g; but they are absent in bishomoaromatic structure 10d, where cyano groups replace the phenyl groups at C‐2 and C‐6 in 10g.

State selective production of phosphorus ions via multiphoton ionization of atomic phosphorus

The (2+1) resonance‐enhanced multiphoton ionization spectrum of phosphorus atoms is reported for the wavelength range 300–317 nm. Atomic phosphorus is formed by multiphoton photodissociation of phosphorus tribromide vapor. Photoelectron spectroscopy conducted at phosphorus ionization resonances produces pure populations of P+(3PJ) and P+(1D2) ions. Production of a mixture of phosphorus ionic states indicates a clear propensity to preserve the ion core electron configuration upon ionization of phosphorus. Four spin‐changing transitions are assigned supported by photoelectron spectral data.

Characterization of the structures of phosphodiesterase 10 binding with adenosine 3',5'-monophosphate and guanosine 3',5'-monophosphate by hybrid quantum mechanical/molecular mechanical calculations.

Quantum mechanical/molecular mechanical (QM/MM) geometry optimizations of the X-ray crystal structures of PDE10-AMP (PDB code 2OUN ) and PDE10-GMP (PDB code 2OUQ ) complexes have been performed to characterize the state of the AMP and GMP products, respectively. Results show that only one phosphate oxygen atom (O1) is protonated for both AMP and GMP product complexes. In addition, QM/MM calculations have resolved the orientation of the amide group of Gln726 in PDE10-GMP which was in conflict with the assignment of the guanine group of GMP in the X-ray crystal structure. Calculations reveal that the amide oxygen and nitrogen atom of Gln726 are rotated 180 degrees, resulting in two strong hydrogen bonds formed between the amide group of Gln726 and the guanine group of GMP. Binding free energy calculations for both QM/MM-optimized structures confirm the new conformational assignment of Gln726 in PDE10-GMP. The calculated binding free energy of the rotated structure is approximately 22 kcal/mol lower than the X-ray crystal assignment. The lower energy is mainly derived from the formation of two hydrogen bonds between the amide group of Gln726 and the guanine group of GMP. This implies that the orientation of the amide oxygen and nitrogen atoms in PDE10-AMP is different from PDE10-GMP. Finally, our results help to understand why PDE10 can hydrolyze both cAMP and cGMP.

Charge exchange reactions of state-selected sulfur ions with OCS

Abstract Sulfur ions in the 2 D o J excited state are observed to charge exchange with OCS molecules. These excited ions are created using resonantly enhanced multiphoton ionization of sulfur atoms generated from photodissociation of parent OCS. Evidence for ionic state-selection is documented with photoelectron spectroscopy. Ground state sulfur ions produced via two-photon autoionization through the 3s 2 3p 3 5p 1 P 1 state at 87624 cm −1 do not exhibit charge exchange reactions under identical conditions.