Theoretical Conformational Analysis in the Determination of Productive Conformations of Substrates for Acetylcholinesterase and Butyrylcholinesterase

All the equilibrium conformations of 34 analogues of acetylcholine (ACh) with the general formula R-C(O)O-Alk-N⁺(CH₃)₃ are calculated by the method of molecular mechanics. In the series R-C(O)O-(CH₂)₂-N⁺(CH₃)₃, a reliable correlation is found between the molecular volume of the substrate and the rate of its hydrolysis by acetylcholinesterase (AChE); the absence of such a correlation is demonstrated for butyryl-cholinesterase (BChE). Theoretical conformational analysis confirms that the completely extended tt conformation of ACh is productive for the hydrolysis by AChE, which agrees with the results of X-ray analysis of AChE. AChE is shown to hydrolyze only those substrates that form equilibrium conformers compatible in the mutual arrangement of trimethylammonium group, carbonyl carbon, and carbonyl oxygen with the tt conformation of ACh; in this case, the rate of substrate hydrolysis depends on the total population of these conformers. A reliable correlation was found between the population of the semifolded (tg^?) conformation of the choline moiety of substrate molecules and rate of their BChE hydrolysis. In a series of CH₃-C(O)O-Alk-N⁺(CH₃)₃, the rate of BChE hydrolysis is demonstrated to depend on the total population of conformations compatible in the mutual arrangement of functionally important atoms with the tg^? conformation of ACh. The tg^? conformation of ACh is concluded to be productive for BChE hydrolysis. Similar orientations of the substrate molecules relative to the catalytic triads of both AChE and BChE are proven to coincide upon the substrate productive sorption in their active sites. It is hypothesized that the sorption stage is rate-limiting in cholinesterase hydrolysis and the enzyme hydrolyzes the ACh molecule in its energetically favorable conformation.     

Low Resolution Structural Studies Indicate that the Activator of Hsp90 ATPase 1 (Aha1) of Leishmania braziliensis Has an Elongated Shape Which Allows Its Interaction with Both N- and M-Domains of Hsp90

The Hsp90 molecular chaperone is essential for protein homeostasis and in the maturation of proteins involved with cell-cycle control. The low ATPase activity of Hsp90 is critical to drive its functional cycle, which is dependent on the Hsp90 cochaperones. The Activator of Hsp90 ATPase-1 (Aha1) is a protein formed by two domains, N- and C-terminal, that stimulates the Hsp90 ATPase activity by several folds. Although the relevance of Aha1 for Hsp90 functions has been proved, as well as its involvement in the desensitization to inhibitors of the Hsp90, the knowledge on its overall structure and behavior in solution is limited. In this work we present the functional and structural characterization of Leishmania braziliensis Aha1 (LbAha1). This protozoan is the causative agent of cutaneous and mucocutaneous leishmaniasis, a neglected disease. The recombinant LbAha1 behaves as an elongated monomer and is organized into two folded domains interconnected by a flexible linker. Functional experiments showed that LbAha1 interacts with L. braziliensis Hsp90 (LbHsp90) with micromolar dissociation constant in a stoichiometry of 2 LbAha1 to 1 LbHsp90 dimer and stimulates 10-fold the LbHsp90 ATPase activity showing positive cooperativity. Furthermore, the LbHsp90::LbAha1 complex is directed by enthalphy and opposed by entropy, probably due to the spatial freedom restrictions imposed by the proteins’ interactions. Small-angle X-ray scattering data allowed the reconstruction of low resolution models and rigid body simulations of LbAha1, indicating its mode of action on LbHsp90. Western blot experiments allowed Aha1 identification (as well as Hsp90) in three Leishmania species at two temperatures, suggesting that Aha1 is a cognate protein. All these data shed light on the LbAha1 mechanism of action, showing that it has structural dimensions and flexibility that allow interacting with both N-terminal and middle domains of the LbHsp90.     

Studies of the thyrotropin-releasing factor. II. Conformations of TRF and some analogs

The conformation of the thyrotropin-releasing factor (TRF) and four analogs have been studied by the CNDO/2 molecular orbital method. The N^δ-protonated tautomer of TRF is predicted to be the more stable of the two tautomeric forms; however, it is postulated that the N^ε-tautomer possesses the most active minimum-energy conformation. The peptide backbone for the five compounds remains nearly constant. The conformations predicted from model fragments are very near to those found for the full compound.     

Genetic and Biochemical Studies on the Formation of Protease in Aspergillus sojae

The mutant strain X816 synthesizing protease and amylase at high rates was crossed with original strain K.S. which is characteristic of abundant sporulation and stable growth, for the purpose of breeding a new koji mold endowed with both parental merits. Diploid strains obtained from these crosses show the intermeadiate character in general both in the formation of these enzymes and in sporulation.

In this paper, the genetic characters of these diploid strains as well as the mode of changes of these enzyme activities during hybrid formation are described.     

N-琥珀酰壳聚糖固定化中性蛋白酶的制备及性质研究

以N-琥珀酰壳聚糖为载体固定中性蛋白酶,研究了固定化酶的适宜温度、pH、热稳定性和酸碱稳定性等酶学性质,同时对固定化酶和游离酶的红外光谱图作了分析比较.结果表明:中性蛋白酶经固定化后,最适酶反应pH由7升至8,最适温度没有改变,仍为50℃,所得固定化酶具有较宽的酸碱稳定性范围,在pH 7～9都保持较高活力,并且同定化酶的热稳定性比游离酶有较大的提高.红外光谱分析表明,酶固定化前后的红外光谱图的部分特征峰有较大的差异.     

Theoretical studies on peptidoglycans. II. Conformations of the disaccharide–peptide subunit and the three-dimensional structure of peptidoglycan

Possible conformations of the disaccharide–peptide subunit of peptidoglycan (of Staphylococcus aureus or Micrococcus luteus) have been studied by an energy-minimization procedure. The favored conformation of the disaccharide N-acetyl-glucosaminyl-β(1–4)-N-acetylmuramic acid (NAG-NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three-dimensional arrangement of peptidoglycan in the bacterial cell wall.     

A Measure of the Signal-to-Noise Ratio of Microarray Samples and Studies Using Gene Correlations

Background

The quality of gene expression data can vary dramatically from platform to platform, study to study, and sample to sample. As reliable statistical analysis rests on reliable data, determining such quality is of the utmost importance. Quality measures to spot problematic samples exist, but they are platform-specific, and cannot be used to compare studies.

Results

As a proxy for quality, we propose a signal-to-noise ratio for microarray data, the “Signal-to-Noise Applied to Gene Expression Experiments”, or SNAGEE. SNAGEE is based on the consistency of gene-gene correlations. We applied SNAGEE to a compendium of 80 large datasets on 37 platforms, for a total of 24,380 samples, and assessed the signal-to-noise ratio of studies and samples. This allowed us to discover serious issues with three studies. We show that signal-to-noise ratios of both studies and samples are linked to the statistical significance of the biological results.

Conclusions

We showed that SNAGEE is an effective way to measure data quality for most types of gene expression studies, and that it often outperforms existing techniques. Furthermore, SNAGEE is platform-independent and does not require raw data files. The SNAGEE R package is available in BioConductor.     

Studies of aberrant phyllotaxy1 Mutants of Maize Indicate Complex Interactions between Auxin and Cytokinin Signaling in the Shoot Apical Meristem

One of the most fascinating aspects of plant morphology is the regular geometric arrangement of leaves and flowers, called phyllotaxy. The shoot apical meristem (SAM) determines these patterns, which vary depending on species and developmental stage. Auxin acts as an instructive signal in leaf initiation, and its transport has been implicated in phyllotaxy regulation in Arabidopsis (Arabidopsis thaliana). Altered phyllotactic patterns are observed in a maize (Zea mays) mutant, aberrant phyllotaxy1 (abph1, also known as abphyl1), and ABPH1 encodes a cytokinin-inducible type A response regulator, suggesting that cytokinin signals are also involved in the mechanism by which phyllotactic patterns are established. Therefore, we investigated the interaction between auxin and cytokinin signaling in phyllotaxy. Treatment of maize shoots with a polar auxin transport inhibitor, 1-naphthylphthalamic acid, strongly reduced ABPH1 expression, suggesting that auxin or its polar transport is required for ABPH1 expression. Immunolocalization of the PINFORMED1 (PIN1) polar auxin transporter revealed that PIN1 expression marks leaf primordia in maize, similarly to Arabidopsis. Interestingly, maize PIN1 expression at the incipient leaf primordium was greatly reduced in abph1 mutants. Consistently, auxin levels were reduced in abph1, and the maize PIN1 homolog was induced not only by auxin but also by cytokinin treatments. Our results indicate distinct roles for ABPH1 as a negative regulator of SAM size and a positive regulator of PIN1 expression. These studies highlight a complex interaction between auxin and cytokinin signaling in the specification of phyllotactic patterns and suggest an alternative model for the generation of altered phyllotactic patterns in abph1 mutants. We propose that reduced auxin levels and PIN1 expression in abph1 mutant SAMs delay leaf initiation, contributing to the enlarged SAM and altered phyllotaxy of these mutants.     

The Semiquinone-Iron Complex of Photosystem II: Structural Insights from ESR and Theoretical Simulation; Evidence that the Native Ligand to the Non-Heme Iron Is Carbonate

The semiquinone-iron complex of photosystem II was studied using electron spin resonance (ESR) spectroscopy and density functional theory calculations. Two forms of the signal were investigated: 1), the native g ∼ 1.9 form; and 2), the g ∼ 1.84 form, which is well known in purple bacterial reaction centers and occurs in photosystem II when treated with formate. The g ∼ 1.9 form shows low- and high-field edges at g ∼ 3.5 and g < 0.8, respectively, and resembles the g ∼ 1.84 form in terms of shape and width. Both types of ESR signal were simulated using the theoretical approach used previously for the BRC complex, a spin Hamiltonian formalism in which the semiquinone radical magnetically interacts (J ∼ 1 cm⁻¹) with the nearby high-spin Fe²⁺. The two forms of ESR signal differ mainly by an axis rotation of the exchange coupling tensor (J) relative to the zero-field tensor (D) and a small increase in the zero-field parameter D (∼6 cm⁻¹). Density functional theory calculations were conducted on model semiquinone-iron systems to identify the physical nature of these changes. The replacement of formate (or glutamate in the bacterial reaction centers) by bicarbonate did not result in changes in the coupling environment. However, when carbonate (CO₃²⁻) was used instead of bicarbonate, the exchange and zero-field tensors did show changes that matched those obtained from the spectral simulations. This indicates that 1), the doubly charged carbonate ion is responsible for the g ∼ 1.9 form of the semiquinone-iron signal; and 2), carbonate, rather than bicarbonate, is the ligand to the iron.