Toward Comprehensive Allosteric Control over Protein Activity

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Regulation of Prostaglandin E2 Receptor Binding Activity in Porcine Temporal Cortex by Protein Phosphorylation

Regulation of prostaglandin (PG) E2 receptors was investigated in a 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate-solubilized fraction from the synaptic membrane of porcine temporal cortex. The fraction was preincubated with exogenous protein kinases, and then the binding of PGE2 was measured. PGE2 binding was increased approximately twofold by pretreatment with the catalytic subunit of cyclic AMP-dependent protein kinase (A kinase) or calmodulin-dependent protein kinase II but not by that with protein kinase C. The increase was dependent on the ATP concentration, with ED50 values being close to the Km values of these protein kinases. Protein kinase inhibitors specific for A kinase and for calmodulin-dependent protein kinase II abolished the effect in a dose-dependent manner, with IC50 values being similar to those reported. Further study using the catalytic subunit of A kinase revealed that the maximal binding capacity apparently increased without affecting the affinity and the rate constants for association and dissociation. On the other hand, acid phosphatase treatment reduced the binding activity to the level of nonspecific binding. In addition, treatment by A kinase did not affect the binding of guanosine 5'-(3-thiotriphosphate) by the GTP-binding proteins and the activation of adenylate cyclase mediated by stimulatory guanine nucleotide-binding regulatory protein, and therefore the phosphorylation is believed to occur on the receptor protein. The results suggest that the PGE2 receptor can take active phosphorylated and inactive dephosphorylated forms, of which only the phosphorylated one can bind PGE2.     

ADAM19 在小鼠睾丸发育中的时空表达

目的 阐明含有去整合素和金属蛋白酶结构域的跨膜蛋白19(ADAM19)在小鼠睾丸发育中的作用.方法 采用半定量RT-PCR和免疫组化两种实验方法,分别检测ADAM19 mRNA和蛋白质在小鼠睾丸发育中的时空表达.结果 ①最早在胚胎发育的15.5 d才能检测到ADAM19 mRNA的表达,后其表达随着胚胎发育天数的增加而逐渐升高,到围产期表达水平达到最高.出生后,ADAM19 mRNA的表达呈现显著下降的趋势,到成体睾丸中就几乎检测不到ADAM19的表达.②和其mRNA表达变化趋势一样,ADAM19蛋白也是首次在胚胎发育的15.5 d被检测到,一直持续存在到出生后一周,一周后则几乎检测不到;阳性表达信号主要定位在睾丸的曲细精管(睾索)中.结论 ADAM19 在小鼠睾丸中的表达具有显著的发育依赖性.     

QAUST: Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how biological systems operate. Here, we propose a novel method, Quantitative Annotation of Unknown STructure (QAUST), to infer protein functions, specifically Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. QAUST uses three sources of information: structure information encoded by global and local structure similarity search, biological network information inferred by protein–protein interaction data, and sequence information extracted from functionally discriminative sequence motifs. These three pieces of information are combined by consensus averaging to make the final prediction. Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation (CAFA) benchmark set. The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading. We further demonstrate that a previously unknown function of human tripartite motif-containing 22 (TRIM22) protein predicted by QAUST can be experimentally validated.     

The N Terminus of Pro-endothelial Monocyte-activating Polypeptide II (EMAP II) Regulates Its Binding with the C Terminus,Arginyl-tRNA Synthetase,and Neurofilament Light Protein

Pro-endothelial monocyte-activating polypeptide II (EMAP II), one component of the multi-aminoacyl tRNA synthetase complex, plays multiple roles in physiological and pathological processes of protein translation, signal transduction, immunity, lung development, and tumor growth. Recent studies have determined that pro-EMAP II has an essential role in maintaining axon integrity in central and peripheral neural systems where deletion of the C terminus of pro-EMAP II has been reported in a consanguineous Israeli Bedouin kindred suffering from Pelizaeus-Merzbacher-like disease. We hypothesized that the N terminus of pro-EMAP II has an important role in the regulation of protein-protein interactions. Using a GFP reporter system, we defined a putative leucine zipper in the N terminus of human pro-EMAP II protein (amino acid residues 1–70) that can form specific strip-like punctate structures. Through GFP punctum analysis, we uncovered that the pro-EMAP II C terminus (amino acids 147–312) can repress GFP punctum formation. Pulldown assays confirmed that the binding between the pro-EMAP II N terminus and its C terminus is mediated by a putative leucine zipper. Furthermore, the pro-EMAP II 1–70 amino acid region was identified as the binding partner of arginyl-tRNA synthetase, a polypeptide of the multi-aminoacyl tRNA synthetase complex. We also determined that the punctate GFP pro-EMAP II 1–70 amino acid aggregate colocalizes and binds to the neurofilament light subunit protein that is associated with pathologic neurofilament network disorganization and degeneration of motor neurons. These findings indicate the structure and binding interaction of pro-EMAP II protein and suggest a role of this protein in pathological neurodegenerative diseases.     

Validation and Quality Control of Protein Microarray-based Analytical Methods

Protein microarray technology is used mainly in the research laboratory and it is being used to uncover important diagnostic and prognostic markers that may one day emerge as routine clinical laboratory tests. It is important that these methods are subject to control procedures, in order to ensure that data of the highest quality are obtained. If quality is not controlled, the assay may yield erroneous results that would mask or confound meaningful diagnostic or prognostic associations. This chapter surveys the range of strategies designed to assure the analytical quality of protein microarray methods and it also highlights some of the potential pitfalls when moving these arrays into routine clinical practice. With the development of appropriate quality control and assurance measures, we anticipate protein microarray-based assays will be of substantial benefit in the future practice of laboratory medicine.     

Differential Regulation of Arylalkylamine N-Acetyltransferase Activity in Chicken Retinal Ganglion Cells by Light and Circadian Clock

Retinal ganglion cells (RGCs) contain circadian clocks driving melatonin synthesis during the day, a subset of these cells acting as nonvisual photoreceptors sending photic information to the brain. In this work, the authors investigated the temporal and light regulation of arylalkylamine N-acetyltransferase (AA-NAT) activity, a key enzyme in melatonin synthesis. The authors first examined this activity in RGCs of wild-type chickens and compared it to that in photoreceptor cells (PRs) from animals maintained for 48?h in constant dark (DD), light (LL), or regular 12-h:12-h light-dark (LD) cycle. AA-NAT activity in RGCs displayed circadian rhythmicity, with highest levels during the subjective day in both DD and LL as well as in the light phase of the LD cycle. In contrast, AA-NAT activity in PRs exhibited the typical nocturnal peak in DD and LD, but no detectable oscillation was observed under LL, under which conditions the levels were basal at all times examined. A light pulse of 30–60?min significantly decreased AA-NAT activity in PRs during the subjective night, but had no effect on RGCs during the day or night. Intraocular injection of dopamine (50 nmol/eye) during the night to mimic the effect of light presented significant inhibition of AA-NAT activity in PRs compared to controls but had no effect on RGCs. The results clearly demonstrate that the regulation of the diurnal increase in AA-NAT activity in RGCs of chickens undergoes a different control mechanism from that observed in PRs, in which the endogenous clock, light, and dopamine exhibited differential effects. (Author correspondence: mguido@fcq.unc.edu.ar)     

Light Regulatilon of the Synthesis of Ribulose 1,5-Bisphosphate Carboxylase and Fructose 1, 6-Bisphosphatase

The activity of ribulose 1,5-bisphosphate carboxylase (RuBPCase, E. C. 4. 1. 1. 395, fructose 1,6-bisphosphatase (FBPase, E. C. 3. 1. 3. 11) and sedoheptulose 1,7-bisphosphatase (SBPase, E. C. 3. 1. 3. 37) was assayed in the etiolated cotyledons of Brassica juncea after red light or far- red light stimulation. There seemed to be a light-sensitive phase in the course of germination as indicated by the response of leaves to light. During this phase red light stimulated the synthesis of RuBPCase and FBPase, but not SBPase. This effect of red light could be reversed by farred light. Therefore, the initiation of the synthesis of the two enzymes was mediated by phytochrome. The amount of enzyme synthesized was not concerned with the number of light quanta. Phytochrome is only involved in the initiation of the synthesis of certain enzymes, but whether the synthesis will proceed continuosely ro not depends on many other factors, e. g. the availability of substrate and energy.     

Effect of Zinc on the Contents of Tomato Chloroplast DNA,RNA, Protein and Chl-Protein Complexes in Relation to Light

Changes of chloroplast DNA, RNA and protein contents in normal andzinc deficient tomato plants grown under different light intensity were studied in thispaper. It was shown that there is no much difference between normal and zinc deficient chloroplast DNA, RNA and protein e0ntents when the plants were grown underlower light intensity, while the DNA, RNA and protein contents of zinc deficient plantsdecreased dramatically under higher light intensity. The DNA and protein contentsof normal plants increased when light intensity was increased from 18000 lx to 45000 lx.The P700 Chl a-protein complexes and light harvesting Chl a/b-protein complexes of zincdeficient plants decreased seriously under higher light intensity.     

Spatial and Temporal Control of Hyperthermia Using Real Time Ultrasonic Thermal Strain Imaging with Motion Compensation,Phantom Study

Mild hyperthermia has been successfully employed to induce reversible physiological changes that can directly treat cancer and enhance local drug delivery. In this approach, temperature monitoring is essential to avoid undesirable biological effects that result from thermal damage. For thermal therapies, Magnetic Resonance Imaging (MRI) has been employed to control real-time Focused Ultrasound (FUS) therapies. However, combined ultrasound imaging and therapy systems offer the benefits of simple, low-cost devices that can be broadly applied. To facilitate such technology, ultrasound thermometry has potential to reliably monitor temperature. Control of mild hyperthermia was previously achieved using a proportional-integral-derivative (PID) controller based on thermocouple measurements. Despite accurate temporal control of heating, this method is limited by the single position at which the temperature is measured. Ultrasound thermometry techniques based on exploiting the thermal dependence of acoustic parameters (such as longitudinal velocity) can be extended to create thermal maps and allow an accurate monitoring of temperature with good spatial resolution. However, in vivo applications of this technique have not been fully developed due to the high sensitivity to tissue motion. Here, we propose a motion compensation method based on the acquisition of multiple reference frames prior to treatment. The technique was tested in the presence of 2-D and 3-D physiological-scale motion and was found to provide effective real-time temperature monitoring. PID control of mild hyperthermia in presence of motion was then tested with ultrasound thermometry as feedback and temperature was maintained within 0.3°C of the requested value.     

Activity, inactivity, and screen time in relation to weight and fatness over adolescence in girls

Objective: The impact of activity and inactivity on relative weight and fatness change are best evaluated longitudinally. We examined the longitudinal relationship of physical activity, inactivity, and screen time with relative weight status and percentage body fat (%BF) and explored how it differed by parental overweight status. Research Methods and Procedures: Non‐obese pre‐menarcheal girls (173), 8 to 12 years old, were followed until 4 years post‐menarche. %BF, BMI z‐score, and time spent sleeping, sitting, standing, walking, and in vigorous activity were assessed annually. We developed a physical activity index to reflect time and intensity of activity. Inactivity was defined as the sum of time spent sleeping, sitting, and standing. Screen time was defined as time spent viewing television, videotapes, or playing video games. Parental overweight was defined as at least one parent with BMI > 25. Results: In separate linear mixed effects models, activity, inactivity, and screen time were unrelated to BMI z‐score longitudinally, with and without accounting for parental overweight. After controlling for parental overweight, activity was inversely related (p < 0.001), and inactivity was directly related (p < 0.035) to increased %BF longitudinally. Screen time was unrelated to %BF change. With stratification for parental overweight, effects of activity and inactivity on %BF were observed only among girls with at least one overweight parent. Discussion: In this cohort of initially non‐overweight girls, activity and inactivity were related to accrual of BF over adolescence, particularly among children with at least one overweight parent. These results suggest that girls with a family history of overweight represent a target population of high priority for interventions around physical activity and inactivity.     

Identification of RFPL3 Protein as a Novel E3 Ubiquitin Ligase Modulating the Integration Activity of Human Immunodeficiency Virus,Type 1 Preintegration Complex Using a Microtiter Plate-based Assay

Integration, one of the hallmarks of retrovirus replication, is mediated by a nucleoprotein complex called the preintegration complex (PIC), in which viral DNA is associated with many protein components that are required for completion of the early phase of infection. A striking feature of the PIC is its powerful integration activity in vitro. The PICs from a freshly isolated cytoplasmic extract of infected cells are able to insert viral DNA into exogenously added target DNA in vitro. Therefore, a PIC-based in vitro assay is a reliable system for assessing protein factors influencing retroviral integration. In this study, we applied a microtiter plate-based in vitro assay to a screening study using a protein library that was produced by the wheat germ cell-free protein synthesis system. Using a library of human E3 ubiquitin ligases, we identified RFPL3 as a potential stimulator of human immunodeficiency virus, type 1 (HIV-1) PIC integration activity in vitro. This enhancement of PIC activity by RFPL3 was likely to be attributed to its N-terminal RING domain. To further understand the functional role of RFPL3 in HIV infection, we created a human cell line overexpressing RFPL3. Immunoprecipitation analysis revealed that RFPL3 was associated with the human immunodeficiency virus, type 1 PICs in infected cells. More importantly, single-round HIV-1 infection was enhanced significantly by RFPL3 expression. Our proteomic approach displays an advantage in the identification of new cellular proteins affecting the integration activity of the PIC and, therefore, contributes to the understanding of functional interaction between retroviral integration complexes and host factors.     

V3 Stain-free Workflow for a Practical,Convenient, and Reliable Total Protein Loading Control in Western Blotting

The western blot is a very useful and widely adopted lab technique, but its execution is challenging. The workflow is often characterized as a "black box" because an experimentalist does not know if it has been performed successfully until the last of several steps. Moreover, the quality of western blot data is sometimes challenged due to a lack of effective quality control tools in place throughout the western blotting process. Here we describe the V3 western workflow, which applies stain-free technology to address the major concerns associated with the traditional western blot protocol. This workflow allows researchers: 1) to run a gel in about 20-30 min; 2) to visualize sample separation quality within 5 min after the gel run; 3) to transfer proteins in 3-10 min; 4) to verify transfer efficiency quantitatively; and most importantly 5) to validate changes in the level of the protein of interest using total protein loading control. This novel approach eliminates the need of stripping and reprobing the blot for housekeeping proteins such as β-actin, β-tubulin, GAPDH, etc. The V3 stain-free workflow makes the western blot process faster, transparent, more quantitative and reliable.     

采用关键点控制和反馈调节,提高微生物学实验课质量

将全面质量管理理论引入微生物学实验课教学,形成以关键点控制和反馈调节为核心的教学质量保障系统,实践证明,可有效地促进学生积极思考,提高实验技能。对教学过程中“关键点”．“关键点控制”的含义和特性以及“反馈信号”、“反馈调节”的含义和类型做了系统的阐述。以具体实验为例,详细说明了实验课教学中关键点控制和反馈调节的实施过程,对于保证教学质量和客观、公正地分析评价教学效果具有重要意义。     

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription

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