Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.conformational transition state ͉ domain movement ͉ induced fit ͉ minimum action pathway ͉ nonequilibrium molecular dynamics

BackgroundD-phenylglycine aminotransferase (D-PhgAT) of Pseudomonas stutzeri ST-201 catalyzes the reversible stereo-inverting transamination potentially useful in the application for synthesis of D-phenylglycine and D-4-hydroxyphenylglycine using L-glutamate as a low cost amino donor substrate in one single step. The enzyme is a relatively hydrophobic homodimeric intracellular protein difficult to express in the soluble functionally active form. Over-expression of the dpgA gene in E. coli resulted in the majority of the D-PhgAT aggregated into insoluble inclusion bodies that failed to be re-natured. Expression in Pichia pastoris was explored as an alternative route for high level production of the D-PhgAT.ResultsIntracellular expression of the codon-optimized synthetic dpgA gene under the PAOX1 promoter in P. pastoris resulted in inactive D-PhgAT associated with insoluble cellular fraction and very low level of D-PhgAT activity in the soluble fraction. Manipulation of culture conditions such as addition of sorbitol to induce intracellular accumulation of osmolytes, addition of benzyl alcohol to induce chaperone expression, or lowering incubation temperature to slow down protein expression and folding rates all failed to increase the active D-PhgAT yield. Co-expression of E. coli chaperonins GroEL-GroES with the D-PhgAT dramatically improved the soluble active enzyme production. Increasing gene dosage of both the dpgA and those of the chaperones further increased functional D-PhgAT yield up to 14400-fold higher than when the dpgA was expressed alone. Optimization of cultivation condition further increased D-PhgAT activity yield from the best co-expressing strain by 1.2-fold.ConclusionsThis is the first report on the use of bacterial chaperones co-expressions to enhance functional intracellular expression of bacterial enzyme in P. pastoris. Only two bacterial chaperone genes groEL and groES were sufficient for dramatic enhancement of functionally active D-PhgAT expression in this yeast. With the optimized gene dosage and chaperone combinations, P. pastoris can be attractive for intracellular expression of bacterial proteins since it can grow to a very high cell density which is translated into the higher volumetric product yield than the E. coli or other bacterial systems.

d-Phenylglycine aminotransferase (d-PhgAT) catalyzes the reversible transamination of d-phenylglycine to l-glutamate with 2-oxoglutarate as the amino-group acceptor. Crystals of substrate-free Pseudomonas stutzeri d-PhgAT bound to the cofactor pyridoxal-5'-phosphate (PLP) were obtained by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 75.155, c = 147.554 A. The asymmetric unit contains one molecule of d-PhgAT and has a solvent content of 50.0%. A complete native X-ray diffraction data set was collected from a single crystal at 100 K to a resolution of 2.3 A.

PurposeTo illustrate the structure–function relationship of compressive optic neuropathy (CON) at the time of diagnosis.Patients and methodsThirty-two eyes of newly diagnosed suprasellar CON and 60 healthy eyes were included in the study. The peripapillary retinal nerve fiber layer (RNFL) thickness and macular ganglion cell-inner plexiform layer (GCIPL) thickness were obtained using Cirrus spectral domain optical coherence tomography (SD-OCT). CON eyes were stratified based on the similar degree and pattern of both RNFL and GCIPL.ResultsFrom 32 eyes of newly diagnosed suprasellar CON eyes, 27 eyes had a predominantly nasal hemiretina thinning of macular GCIPL, 4 eyes showed a generalized macular thinning, and 1 eye showed a predominantly superior macular thinning. The corresponding temporal peripapillary RNFL thinning with nasal hemiretina GCIPL thinning were inconsistently manifested. Structure–function analysis of stratified CON eyes with similar thinning profiles showed that a range rather than a fixed value of visual field loss based on mean deviation (MD) index was associated to each thinning profile. The maximal limit of visual field loss range was ubiquitously nonrestricted to any structural thinning profile. While the minimal limit of the associated MD range was gradually reduced from 0 to about −16.0 dB, the nasal hemiretina macular GCIPL thinning was the only manifestation and decreased from 75 to 45 µm. However, the different degrees of temporal hemiretina macular GCIPL and superior–inferior peripapillary RNFL thinning were only seen in 10 of 32 eyes of which their nasal hemiretina GCIPL and temporal RNFL thinning had reached significant thinning. Interestingly when present, the minimal limit of associated MD range continued to decrease from −16.0 to −32.0 dB.ConclusionCON eyes can present with variable structure and function relationship at the time of diagnosis. Using structural parameters at the time of diagnosis to predict the prognosis should be used with caution.