Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway

Mutations in DNA polymerase β (pol β) have been associated with approximately 30% of human tumors. The E295K mutation of pol β has been linked to gastric carcinoma via interference with base excision repair. To interpret the different behavior of E295K as compared to wild-type pol β in atomic and energetic detail, we resolve a binary crystal complex of E295K at 2.5 ? and apply transition path sampling (TPS) to delineate the closing pathway of the E295K pol β mutant. Conformational changes are important components in the enzymatic pathway that lead to and ready the enzyme for the chemical reaction. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol β in terms of the individual transition states along the pathway, associated energies, and the active site conformation in the final closed form of the mutant. In particular, the closed state of E295K has a more distorted active site than the active site in the wild-type pol β. In addition, the total energy barrier in the conformational closing pathway is 65 ± 11 kJ/mol, much higher than that estimated for both correct (e.g., G:C) and incorrect (e.g., G:A) wild-type pol β systems (42 ± 8 and 45 ± 7 kJ/mol, respectively). In particular, the rotation of Arg258 is the rate-limiting step in the conformational pathway of E295K due to unfavorable electrostatic and steric interactions. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Interestingly, however, following the closing of the thumb but prior to the rotation of Arg258, the E295K mutant complex has a similar energy level as compared to the wild-type pol β. This suggests that the E295K mutant may associate with DNA with similar affinity, but it may be hampered in continuing the process of chemistry. Supporting experimental data come from the observation that the catalytic activity of wild-type pol β is hampered when E295K is present: this may arise from the competition between E295K and wild-type enzyme for the DNA. These combined results suggest that the low insertion efficiency of E295K mutant as compared to wild-type pol β may be related to a closed form distorted by unfavorable electrostatic and steric interactions between Arg258 and other key residues. The active site is thus less competent for proceeding to the chemical reaction, which may also involve a higher reaction barrier than the wild-type or may not be possible in this mutant. Our analysis also suggests further experiments for other mutants to test the above hypothesis and dissect the roles of steric and electrostatic factors on enzyme behavior.     

A survey of solution techniques for the partially observed Markov decision process

We survey several computational procedures for the partially observed Markov decision process (POMDP) that have been developed since the Monahan survey was published in 1982. The POMDP generalizes the standard, completely observed Markov decision process by permitting the possibility that state observations may be noise-corrupted and/or costly. Several computational procedures presented are convergence accelerating variants of, or approximations to, the Smallwood-Sondik algorithm. Finite-memory suboptimal design results are reported, and new research directions involving heuristic search are discussed.This research was supported by NSF Grant ECS-8708183 and ARO Contract DAAG-29-85-K0089.     

Continuous,on-demand generation and separation of diphenylphosphoryl azide

Diphenylphosphorylazide (DPPA) has been synthesized in microfluidics with near-100% yield in sub-3 minute residence time, affordably, and with a process design that minimizes hazards associated with hydrazoic acid (HN₃) production. A pilot-plant scale continuous process for the on-demand synthesis of diphenylphosphoryl azide (DPPA) that can readily be integrated with subsequent transformations was designed, built, and validated. Using Corning's Low Flow reactor system coupled to a membrane separator and in-line Fourier Transform Infrared (FTIR), DPPA was safely produced at a rate of 1?mol/hr as a 2.0?M anhydrous toluene stream. Continuous FTIR was able to reliably monitor product quality, purity and concentration, showcasing the ease and utility of this continuous flow process for manufacturing common, safe pharmaceutical precursors.     

2.2](4,4′) benzophenono (2,6) naphthalenophane: synthesis,structure, and spectroscopic study

The synthesis of [2.2](4,4′) benzophenono (2,6) naphthalenophane (1), the parent member of a series of stacked sensitizer-acceptor cyclophanes, is reported along with its x-ray structure and the absorption and emission spectra.     

Experimental thermochemical study of two polymethylpyrazine N,N′-dioxide derivatives

The standard (p° = 0.1 MPa) molar enthalpies of formation of crystalline 2,3,5-trimethylpyrazine-1,4-dioxide and 2,3,5,6-tetramethylpyrazine-1,4-dioxide were measured, at T = 298.15 K, by static bomb calorimetry and the standard molar enthalpies of sublimation, at T = 298.15 K, were obtained from Calvet microcalorimetric measurements. These values were used to derive the respective standard molar enthalpies of formation in gaseous phase. The mean N–O bond dissociation enthalpy has been calculated for both compounds.     

New phototriggers: extending the p-hydroxyphenacyl pi-pi absorption range

[equation--see text] Introducing 3-methoxy or 3,5-dimethoxy substituents on the 4-hydroxyphenacyl (pHP) photoremovable protecting group has been explored with two excitatory gamma-amino acids, L-glutamic acid and gamma-amino butyric acid (GABA). These substituents significantly extend the absorption range of the pHP chromophore, e.g., the tail of absorption bands of 2a,b extend above 400 nm, well beyond the absorptions of aromatic amino acids and nucleotides. Irradiation releases the amino acids with rate constants of approximately 10(7) s(-)(1) and appearance efficiencies (Phi(app)) of 0.03-0.04. The photoproducts are formed through the pHP excited triplet and are primarily products of photoreduction and photohydrolysis. 1a,b also rearranged to the phenylacetic acid 3.     

Operational and design considerations for broad area graded barrier quantum well heterostructure lasers grown by metalorganic chemical vapor deposition for high power applications

Graded barrier quantum well heterostructure (GBQWH) broad area lasers have been shown to be capable of high power pulsed and cw operation. In this article, we consider several operational characteristics and design issues associated with broad area graded barrier quantum well heterostructure lasers grown by metalorganic chemical vapor deposition. In particular, the effect of junction heating on emission wavelength for cw device operation and the effects of various buffer layer structures on the material properties and device characteristics of GBQWH structures are addressed. Typical results for high power operation of uncoated broad area laser diodes are also outlined.     

Oxalate/hydrogen peroxide chemiluminescence reaction. A 19F NMR probe of the reaction mechanism

The mechanism of the oxalate/hydrogen peroxide chemiluminescence reaction has been examined by magnetic resonance techniques. Investigation of the reactive intermediates involved in chemiluminescence was carried out with bis(2,6-difluorophenyl)oxalate (DFPO) using 19F NMR to probe its reactions with aqueous hydrogen peroxide. Formation and reactions of the intermediate hydroperoxy oxalate ester B along with the formation of the half ester product C and difluorophenol D were monitored by 19F NMR. When the reaction of DFPO and aqueous hydrogen peroxide was carried out in the presence of dansylphenylalanine, a typical fluorescent analyte, the intensity of the resonance due to the intermediate B was diminished in direct proportion to the concentration of the analyte. Comparison of the time/intensity profile of the chemiluminescence emission with that of the 19F NMR transient suggests that the hydroperoxy oxalate ester B is the likely 'reactive' intermediate, capable of participating in a chemically initiated electron exchange luminescence mechanism.