Computational assessment of folding energy landscapes in heterodimeric coiled coils

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs‐into‐holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes.     

Cardiopulmonary control in sleeping Sprague-Dawley rats treated with hydralazine

Carley, David W., Sinisa M. Trbovic, Alex Bozanich, andMiodrag Radulovacki. Cardiopulmonary control in sleepingSprague-Dawley rats treated with hydralazine. J. Appl.Physiol. 83(6): 1954-1961, 1997.To test thehypothesis that hydralazine can suppress spontaneous sleep-relatedcentral apnea, respiratory pattern, blood pressure, and heart periodwere monitored in Sprague-Dawley rats. In random order and on separatedays, rats were recorded after intraperitoneal injection of1) saline or2) 2 mg/kg hydralazine. Normalizedminute ventilation(NI)declined significantly with transitions from wake tonon-rapid-eye-movement (NREM) sleep (5.1%;P = 0.01) and rapid-eye-movement (REM)sleep (4.2%; P = 0.022).Hydralazine stimulated respiration(NIincreased by 21%; P < 0.03) andeliminated the effect of state onNI. Bloodpressure decreased by 17% after hydralazine, and the correlationbetween fluctuations in mean blood pressure andNI changedfrom strongly positive during control recordings to weakly negativeafter hydralazine (P < 0.0001 foreach). Postsigh and spontaneous apneas were reduced during NREM and REMsleep after hydralazine (P < 0.05 for each). This suppression was strongly correlated with the reductionin blood pressure and with the degree of respiratory stimulation. Weconclude that mild hydralazine-induced hypotension leads to respiratory stimulation and apnea suppression.

     

Impact of war on central nervous system tumors incidence--a 15-year retrospective study in Istria County, Croatia

The aim of study was to analyze epidemiological features of central nervous system (CNS) tumors diagnosed in Istria County, Croatia, with a particular emphasis on incidence dynamics during the wartime (1991-1995). The data were extracted from the medical records of patients with CNS tumors admitted to the Department of Neurology of Pula General Hospital in the period from the 1st January 1986 to the 31st December 2000, N = 364. For calculation of rates, we used data from the 2001 Croatian consensus http://www.dzs.hr/Eng/Census/census2001.htm. Data are presented as counts and incidence rates (IRs) per 100,000 persons-years in the case of annual rates. Annual incidence rates are shown as "raw" incidence rates and smoothed 5-year rolling average rates. The examined patient-related variables were: sex, age, occupation, premorbidity and comorbidity, with a particular emphasis on psychosomatic disorders and negative habits. The analyzed tumor-related variables included clinical manifestation, localization, and applied diagnostic and therapeutic methods. Primary tumors were separated from the metastatic, and the latter were analysed with respect to their site of origin. The lowest incidence of CNS tumors (10 patients) was reported in 1990, and the highest (42 patients) in 1993. The incidence dynamics of CNS tumors showed a rapidly progressive increase over the 1991-1995 period, followed by the return to average values. The access to a better and more readily available diagnostics may only partially explain this phenomenon. Therefore, we analyzed other factors that may have contributed towards the rapid increase in the number of CNS tumors, such as its coincidence with the war or psychotrauma. The results confirm the observational clinical hypothesis of an extreme increase in the number of CNS tumors during the period under consideration.     

Catalysis and linear free energy relationships in aspartic proteases

Aspartic proteases are receiving considerable attention as potential drug targets in several serious diseases, such as AIDS, malaria, and Alzheimer's disease. These enzymes cleave polypeptide chains, often between specific amino acid residues, but despite the common reaction mechanism, they exhibit large structural differences. Here, the catalytic mechanism of aspartic proteases plasmepsin II, cathepsin D, and HIV-1 protease is examined by computer simulations utilizing the empirical valence bond approach in combination with molecular dynamics and free energy perturbation calculations. Free energy profiles are established for four different substrates, each six amino acids long and containing hydrophobic side chains in the P1 and P1' positions. Our simulations reproduce the catalytic effect of these enzymes, which accelerate the reaction rate by a factor of approximately 10(10) compared to that of the corresponding uncatalyzed reaction in water. The calculations elucidate the origin of the catalytic effect and allow a rationalization of the fact that, despite large structural differences between plasmepsin II/cathepsin D and HIV-1 protease, the magnitude of their rate enhancement is very similar. Amino acid residues surrounding the active site together with structurally conserved water molecules are found to play an important role in catalysis, mainly through dipolar (electrostatic) stabilization. A linear free energy relationship for the reactions in the different enzymes is established that also demonstrates the reduced reorganization energy in the enzymes compared to that in the uncatalyzed water reaction.     

Utilization of oil extracted from spent coffee grounds for sustainable production of polyhydroxyalkanoates

Spent coffee grounds (SCG), an important waste product of the coffee industry, contain approximately 15 wt% of coffee oil. The aim of this work was to investigate the utilization of oil extracted from SCG as a substrate for the production of poly(3-hydroxybutyrate) (PHB) by Cupriavidus necator H16. When compared to other waste/inexpensive oils, the utilization of coffee oil resulted in the highest biomass as well as PHB yields. Since the correlation of PHB yields and the acid value of oil indicated a positive effect of the presence of free fatty acids in oil on PHB production (correlation coefficient R ²?=?0.9058), superior properties of coffee oil can be probably attributed to the high content of free fatty acids which can be simply utilized by the bacteria culture. Employing the fed-batch mode of cultivation, the PHB yields, the PHB content in biomass, the volumetric productivity, and the Y _P/S yield coefficient reached 49.4 g/l, 89.1 wt%, 1.33 g/(l h), and 0.82 g per g of oil, respectively. SCG are annually produced worldwide in extensive amounts and are disposed as solid waste. Hence, the utilization of coffee oil extracted from SCG is likely to improve significantly the economic aspects of PHB production. Moreover, since oil extraction decreased the calorific value of SCG by only about 9 % (from 19.61 to 17.86 MJ/kg), residual SCG after oil extraction can be used as fuel to at least partially cover heat and energy demands of fermentation, which should even improve the economic feasibility of the process.     

An Arabidopsis Rhomboid homolog is an intramembrane protease in plants

Regulated intramembrane proteolysis (RIP) is a fundamental mechanism for controlling a wide range of cellular functions. The Drosophila protein Rhomboid-1 (Rho-1) is an intramembrane serine protease that cleaves epidermal growth factor receptor (EGFR) ligands to release active growth factors. Despite differences in the primary structure of Rhomboid proteins, the proteolytic activity and substrate specificity of these enzymes has been conserved in diverse organisms. Here, we show that an Arabidopsis Rhomboid protein AtRBL2 has proteolytic activity and substrate specificity. AtRBL2 cleaved the Drosophila ligands Spitz and Keren, but not similar proteins like TGFalpha, when expressed in mammalian cells, leading to the release of soluble ligands into the medium. These studies provide the first evidence that the determinants of RIP are present in plants.     

Compartmentalization of growth factor receptor signalling

Spatial and temporal separation of signal transduction pathways often determines the specificity in cellular responses. Recent advances have improved our understanding of how growth factor signalling is influenced by the formation of molecular complexes (signalosomes) in distinct cellular compartments. There has also been new insight into the mechanisms that determine the signalling competence of these complexes and their role in receptor endocytosis, retrograde trafficking in neurons and restricted protein biosynthesis, and many examples have been found where signalosome deregulation leads to disease.     

A century of antivenom

Because it primarily affects the poor in undeveloped parts of the world where medical care is often inadequate and insufficient, envenomation is considered a neglected public health issue, despite the existence of antivenom therapy for more than a century. This article provides an overview of the epidemiological situation for important venomous animals, together with achievements in the production, control, technological progress and safety of antivenoms since their discovery.     

Sex and dosing-time dependencies in irinotecan-induced circadian disruption

Circadian disruption accelerates malignant growth; thus, it should be avoided in anticancer therapy. The circadian disruptive effects of irinotecan, a topoisomerase I inhibitor, was investigated according to dosing time and sex. In previous work, irinotecan achieved best tolerability following dosing at zeitgeber time (ZT) 11 in male and ZT15 in female mice, whereas worst toxicity corresponded to treatment at ZT23 and ZT3 in male and female mice, respectively. Here, irinotecan (50 mg/kg intravenous [i.v.]) was delivered at the sex-specific optimal or worst circadian timing in male and female B6D2F1 mice. Circadian disruption was assessed with rest-activity, body temperature, plasma corticosterone, and liver mRNA expressions of clock genes Rev-erbα, Per2, and Bmal1. Baseline circadian rhythms in rest-activity, body temperature, and plasma corticosterone were more prominent in females as compared to males. Severe circadian disruption was documented for all physiology and molecular clock endpoints in female mice treated at the ZT of worst tolerability. Conversely, irinotecan administration at the ZT of best tolerability induced slight alteration of circadian physiology and clock-gene expression patterns in female mice. In male mice, irinotecan produced moderate alterations of circadian physiology and clock-gene expression patterns, irrespective of treatment ZT. However, the average expression of Rev-erbα, Per2, and Bmal1 were down-regulated 2- to 10-fold with irinotecan at the worst ZT, while being minimally or unaffected at the best ZT, irrespective of sex. Corticosterone secretion increased acutely within 2?h with a sex-specific response pattern, resulting in a ZT-dependent phase-advance or -delay in both sex. The mRNA expressions of irinotecan clock-controlled metabolism genes Ce2, Ugt1a1, and Top1 were unchanged or down-regulated according to irinotecan timing and sex. This study shows that the circadian timing system represents an important toxicity target of irinotecan in female mice, where circadian disruption persists after wrongly timed treatment. As a result, the mechanisms underling cancer chronotherapeutics are expectedly more susceptible to disruption in females as compared to males. Thus, the optimal circadian timing of chemotherapy requires precise determination according to sex, and should involve the noninvasive monitoring of circadian biomarkers.