Crystallization chaperone strategies for membrane proteins

From G protein-coupled receptors to ion channels, membrane proteins represent over half of known drug targets. Yet, structure-based drug discovery is hampered by the dearth of available three-dimensional models for this large category of proteins. Other than efforts to improve membrane protein expression and stability, current strategies to improve the ability of membrane proteins to crystallize involve examining many orthologs and DNA constructs, testing the effects of different detergents for purification and crystallization, creating a lipidic environment during crystallization, and cocrystallizing with covalent or non-covalent soluble protein chaperones with an intrinsic high propensity to crystallize. In this review, we focus on this last category, highlighting successes of crystallization chaperones in membrane protein structure determination and recent developments in crystal chaperone engineering, including molecular display to enhance chaperone crystallizability, and end with a novel generic approach in development to target any membrane protein of interest.     

Expression of a self-processing,pathogen resistance-enhancing gene construct in <Emphasis Type="Italic">Arabidopsis</Emphasis>

A gene cassette, p35S-CNO, was designed to express three gene products driven by a single constitutive CaMV 35S promoter. The individual coding regions were linked in frame to produce a single polyprotein, using spacer sequences encoding a specific heptapeptide cleavage recognition site (ENLYFQS) for the nuclear-inclusion-a (NIa) proteinase of tobacco etch virus (TEV). The protein coding sequences used were: a Trichoderma harzinum endochitinase, a truncated NIa proteinase of TEV, and a wheat oxalate oxidase. When p35S-CNO construct was tested in Arabidopsis thaliana, the polyprotein was properly cleaved after translation and the products exhibited functional enzymatic activity in vivo.Revisions requested 17 January 2005; Revisions received 17 January 2005     

Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa

Pyoverdine is the primary siderophore of the gram-negative bacterium Pseudomonas aeruginosa. The pyoverdine region was recently identified as the most divergent locus alignable between strains in the P. aeruginosa genome. Here we report the nucleotide sequence and analysis of more than 50 kb in the pyoverdine region from nine strains of P. aeruginosa. There are three divergent sequence types in the pyoverdine region, which correspond to the three structural types of pyoverdine. The pyoverdine outer membrane receptor fpvA may be driving diversity at the locus: it is the most divergent alignable gene in the region, is the only gene that showed substantial intratype variation that did not appear to be generated by recombination, and shows evidence of positive selection. The hypothetical membrane protein PA2403 also shows evidence of positive selection; residues on one side of the membrane after protein folding are under positive selection. R', previously identified as a type IV strain, is clearly derived from a type III strain via a 3.4-kb deletion which removes one amino acid from the pyoverdine side chain peptide. This deletion represents a natural modification of the product of a nonribosomal peptide synthetase enzyme, whose consequences are predictive from the DNA sequence. There is also linkage disequilibrium between the pyoverdine region and pvdY, a pyoverdine gene separated by 30 kb from the pyoverdine region. The pyoverdine region shows evidence of horizontal transfer; we propose that some alleles in the region were introduced from other soil bacteria and have been subsequently maintained by diversifying selection.     

Resonant ultrasound spectroscopy measurements of the elastic constants of human dentin

The technique of resonant ultrasound spectroscopy (RUS) was used to measure the second-order elastic constants of hydrated human dentin. Specimens were placed between two transducers, and the resonant frequencies of vibration were measured between 0.5 and 1.4 MHz. The elastic constants determined from the measured resonant frequencies in hydrated dentin exhibited slight hexagonal anisotropy, with the stiffest direction being perpendicular to the axis of the tubules (E11 = 25.1GPA) This hexagonal anisotropy was small (E33/E11 = 0.92), and almost disappeared when the specimens were dried. In addition, there was a pronounced anisotropy in the Poisson's ratio of wet dentin: v21 = 0.45; v31 = 0.29. With drying in air, this anisotropy vanished: v21 = v31 = 0.29. The isotropic Young's modulus of dried dentin was 28.1 GPa. RUS shows promise for determining the elastic constants in mineralized tissues.     

Molecular phylogeny and dating reveals an Oligo-Miocene radiation of dry-adapted shrubs (former Tremandraceae) from rainforest tree progenitors (Elaeocarpaceae) in Australia

To better understand the historical biogeography of the southern hemisphere and evolutionary responses of plants to aridity, we undertook a detailed phylogenetic study of the predominantly southern family Elaeocarpaceae sensu lato (including Tremandraceae). Plastid trnL-trnF and nuclear ITS sequence data were analyzed using parsimony and Bayesian methods and molecular evolutionary rates calibrated using the Oligocene fossil record of Elaeocarpus mesocarps to estimate the minimum divergence dates. The results indicate the monophyly of all recognized genera and a placement for the former Tremandraceae (three genera and about 49 species of shrubby, dry-adapted Australian plants) within the widespread predominantly rainforest tree family Elaeocarpaceae (nine genera, over 500 species). The former Tremandraceae clade diverged from its sister (Aceratium + Elaeocarpus + Sericolea) during the Paleocene, after which it underwent a marked acceleration in evolutionary rate. Furthermore, this lineage diversified during the late Miocene, coincident with widespread aridification in Australian environments and extensive radiations of several sclerophyllous groups. The role of dispersal in explaining the current geographical distribution of Elaeocarpaceae is illustrated by Aristotelia. This genus, whose distribution was previously thought to reflect Gondwanan vicariance, is shown to have arrived in New Zealand from Australia at least 6-7 million yr ago.     

On-line measurement of gas production rates

Gas evolution rates represent an important variable to track in biological and certain electrochemical processes. Accurate gas flow rate sensors exist for gas streams possessing a pressure head, such as when pressurized air or oxygen is delivered to a fermentation process. However, these devices impose pressure heads that can inhibit gas production and, therefore, yield false measurements. Examples of effected processes would include electrochemical production of a gas at the electrode (e.g., electrolysis) or anaerobic fermentation (e.g., anaerobic production of methane). In this work, we present an on-line gas measurement technique that measures on-line gas production from an anaerobic microbial process that is continuously fed simulated food waste over a 6-month period. Commentary is given on the sensor's accuracy and ease of use within the context of long-term operation, ability to measure both low and high gas production rates, as well as its potential for process control and system-health monitoring.     

Health-related quality of life and weight loss among overweight and obese U.S. adults, 2001 to 2002

Objective: To examine the prevalence and association of health‐related quality of life (HRQOL) with trying to lose weight and with weight loss practices (eating fewer calories, physical activity, and both) among overweight and obese U.S. adults ≥ 20 years of age. Research Methods and Procedures: This study used data from the 2001 to 2002 National Health and Nutrition Examination Survey, a continuous annual survey of the civilian non‐institutionalized U.S. population. This analysis included those ≥ 20 years of age with BMI ≥ 25 (n = 2578) who responded to four standard HRQOL measures that assessed general health status and recent physical health, mental health, and activity limitation. Results: Among obese men, but not women, there were significant increasing linear trends in the adjusted prevalence of trying to lose weight as physically unhealthy and activity limitation days increased. Regardless of BMI or HRQOL, reducing calories was a common weight loss practice (66% to 86%). Except for recent activity limitation, respondents with BMI ≥ 35 did not generally differ by HRQOL level in the attainment of recommended physical activity either alone or in combination with reduced calories, whereas those in the BMI 25 to 34.9 groups often differed significantly by HRQOL level. Specifically, increased unhealthy or activity limitation days were associated with reduced prevalence of attained physical activity. Discussion: Our findings indicate an association between trying to lose weight and a greater number of unhealthy days reported by obese men, suggesting that these men may be influenced by traditional clinical weight‐loss counseling that is prompted by weight and comorbidity, whereas women had a high prevalence of trying to lose weight irrespective of weight and HRQOL. Assessment of HRQOL, especially measures that evaluate physical domains, could provide subjective information to assist with weight counseling.     

Interactions between PTB RRMs Induce Slow Motions and Increase RNA Binding Affinity

Polypyrimidine tract binding protein (PTB) participates in a variety of functions in eukaryotic cells, including alternative splicing, mRNA stabilization, and internal ribosomal entry site-mediated translation initiation. Its mechanism of RNA recognition is determined in part by the novel geometry of its two C-terminal RNA recognition motifs (RRM3 and RRM4), which interact with each other to form a stable complex (PTB1:34). This complex itself is unusual among RRMs, suggesting that it performs a specific function for the protein. In order to understand the advantage it provides to PTB, the fundamental properties of PTB1:34 are examined here as a comparative study of the complex and its two constituent RRMs. Both RRM3 and RRM4 adopt folded structures that NMR data show to be similar to their structure in PRB1:34. The RNA binding properties of the domains differ dramatically. The affinity of each separate RRM for polypyrimidine tracts is far weaker than that of PTB1:34, and simply mixing the two RRMs does not create an equivalent binding platform. ¹⁵N NMR relaxation experiments show that PTB1:34 has slow, microsecond motions throughout both RRMs including the interdomain linker. This is in contrast to the individual domains, RRM3 and RRM4, where only a few backbone amides are flexible on this time scale. The slow backbone dynamics of PTB1:34, induced by packing of RRM3 and RRM4, could be essential for high-affinity binding to a flexible polypyrimidine tract RNA and also provide entropic compensation for its own formation.     

Reduction of infarct size with D-myo-inositol trisphosphate: role of PI3-kinase and mitochondrial K(ATP) channels

Prophylactic treatment with D-myo-inositol 1,4,5-trisphosphate hexasodium [D-myo-Ins(1,4,5)P3], the sodium salt of the endogenous second messenger Ins(1,4,5)P3, triggers a reduction of infarct size comparable in magnitude to that seen with ischemic preconditioning (PC). However, the mechanisms underlying D-myo-Ins(1,4,5)P3-induced protection are unknown. Accordingly, our aim was to investigate the role of four archetypal mediators implicated in PC and other cardioprotective strategies (i.e., PKC, PI3-kinase/Akt, and mitochondrial and/or sarcolemmal K(ATP) channels) in the infarct-sparing effect of D-myo-Ins(1,4,5)P3. Fifteen groups of isolated buffer-perfused rabbit hearts [5 treated with D-myo-Ins(1,4,5)P3, 5 treated with PC, and 5 control cohorts] underwent 30 min of coronary artery occlusion and 2 h of reflow. One set of control, D-myo-Ins(1,4,5)P3, and PC groups received no additional treatment, whereas the remaining sets were infused with chelerythrine, LY-294002, 5-hydroxydecanoate (5-HD), or HMR-1098 [inhibitors of PKC, PI3-kinase, and mitochondrial and sarcolemmal ATP-sensitive K+ (K(ATP)) channels, respectively]. Infarct size (delineated by tetrazolium staining) was, as expected, significantly reduced in both D-myo-Ins(1,4,5)P3- and PC-treated hearts versus controls. D-myo-Ins(1,4,5)P3-induced cardioprotection was blocked by 5-HD but not HMR-1098, thereby implicating the involvement of mitochondrial, but not sarcolemmal, K(ATP) channels. Moreover, the benefits of D-myo-Ins(1,4,5)P3 were abrogated by LY-294002, whereas, in contrast, chelerythrine had no effect. These latter pharmacological data were corroborated by immunoblotting: D-myo-Ins(1,4,5)P3 evoked a significant increase in expression of phospho-Akt but had no effect on the activation/translocation of the cardioprotective epsilon-isoform of PKC. Thus PI3-kinase/Akt signaling and mitochondrial K(ATP) channels participate in the reduction of infarct size afforded by prophylactic administration of D-myo-Ins(1,4,5)P3.