Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory

Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of conformational sub states in this way both illustrates the degree of conformational convergence in the simulation and reduces the structural data to a tractable subset. The relative movement of structures upon energy minimization was used to estimate the sizes of features on the protein potential energy surface. The structures were analyzed using their pairwise root-mean-square C_α deviations, which gave a global measure of conformational changes that would not be apparent by monitoring single degrees of freedom. At time scales of 0.1 ps, energy minimization detected sharp transitions between energy minima separated by 0.1 Å rms deviation. Larger conformational clusters containing these smaller minima and separated by 0.25 Å were seen at 1 ps time scales. Both of these small features of the conformational landscape were characterized by movements in loop regions associated with small, correlated backbone dihedral angle shifts. On a nanosecond time scale, the main features of the protein energy landscape were clusters separated by over 0.7 Å rms deviation, with only seven of these sub states visited over the 1 ns trajectory. These substates, discernible both before and after energy minimization, differ mainly in a monotonic pivot of the loop residues 11–18 over the course of the simulation. This loop contains lysine 17, which specifically binds to trypsin in the active site. The trajectory did not return to previously visited clusters, indicating that this trajectory has not been shown to have completely sampled the conformational substates available to it. Because the apparent convergence to a single region of conformation space depends on both the time scale of observation and the size of the conformational features examined, convergence must be operationally defined within the context of the simulation. © 1995 Wiley-Liss, Inc.     

Differences Between Right and Left Arm Blood Pressures in the Elderly

Recommendations vary on whether blood pressures should be measured in the right or in the left arm because no frequency distributions for a pressure difference between the arms exist. We took a total of 12 blood pressure determinations in both arms of 174 elderly persons and analyzed the data by a least-squares components of variance method. The mean difference between the arms (right minus left) was 0.93 mm of mercury for systole and 0.70 mm of mercury for diastole. For systole the proportion of persons having arm pressure differences exceeding 10 mm of mercury is 1.4% and that exceeding 7.5 mm of mercury is 6.5%. For most people, the pressure difference between the arms is small.     

Interactions of carbaryl with estuarine bacterial communities

The addition of carbaryl (100g/ml) to a model estuarine ecosystem did not affect the number of bacteria in the sediment, but reduced the diversity (as measured by the rarefaction technique) of the microbial community as compared with a control model ecosystem. Two carbaryltolerant strains of bacteria were isolated from the carbaryl-treated system, but none were isolated from the control system. Bacterial growth and filter paper decomposition in mixed cultures was prevented by 100g/ml carbaryl, but this amount had no effect on the extracellular cellulase of an estuarine isolate. Increasing the amount of organic matter in the medium attenuated the toxicity of carbaryl to pure cultures of an estuarine isolate. The addition of 1, 10, or 100g/ml carbaryl to field plots had no effect on bacterial numbers, diversity, or filter paper decomposition. The amount of carbaryl in sediments exposed to 100g/ml fell below the limit of detection by thin-layer chromatography within 12 hours. In sterile and nonsterile model systems, carbaryl rapidly adsorbed to sediment, and hydrolyzed to 1-naphthol in both sediment and water. Although carbaryl may be toxic to bacteria under some conditions, the amounts that might enter and persist in an estuary are insufficient to have a significant impact on the sediment microbial community.     

Functional characteristics and responses to adrenergic stimulation of isolated heart preparations from hypothermic and hibernating subjects

Contemporary studies of isolated hearts from hibernators and nonhibernators are presented. Original experiments with isolated perfused hamster hearts are reported. Such hearts can maintain left ventricular function at temperatures as low as 7 °C. Generated left ventricular pressure was 40 ± 9 mm Hg and heart rate was 7 ± 1 beats/min. During cooling heart rate dropped dramatically, coronary flow increased, and ventricular pressure decreased initially, plateaued, and then fell as 7 °C was approached. Norepinephrine can cause increased heart rate and left ventricular pressure at 22 and 7 °C. This positive inotropic and chronotropic response was associated with increased cAMP at 30 sec after stimulation at 22 °C but not at 7 °C. Furthermore. cAMP was also not changed at peak response at 7 °C. Isoproterenol increased cAMP content in 37 °C ventricular slices but not at hypothermic temperatures. Possible mechanisms of nonadenylate cyclase mediation of inotropic and chronotropic responses at 7 °C are discussed.     

Interactions of U1 RNP with heterogeneous nuclear RNA in rat Novikoff hepatoma nuclei

Summary The nature of the association of U1 RNA with rapidly sedimenting RNP structures in rat hepatoma nuclei was investigated. The effects of salt and proteinase K treatment on the stability of this bound form of U1 RNA were studied using sucrose density gradient analyses. Quantitation of the amount of U1 RNA remaining associated with large structures after treatment was used to assess the relative contribution of protein-protein(and protein-RNA) versus RNA-RNA interactions. Forty-eight percent of the total nuclear U1 RNA released by sonication was found in a bound form when the sonicate was centrifuged through gradients containing 50 mM NaCl. Fifty percent of this bound U1 RNA remained associated with rapidly sedimenting RNPs when the NaCl concentration was raised to 500 mM. To assess the contribution of protein independent interactions, large RNPs were completely deproteinized and their RNA moieties were then recentrifuged on gradients. By this analysis, 27% of the U1 RNA originally bound to hnRNPs was associated with rapidly sedimenting (>30 S) RNA (at 50 mM NaCl) suggesting their association by RNA-RNA hydrogen bonds. When the concentration of NaCl was 500 mM, 31% of the U1 RNA was associated with large RNA. Hence, approximately 30% of the U1 RNA molecules originally bound (or about 15% of the total nuclear U1 RNA) were found to be associated by RNA-RNA hydrogen bonds while the remainder of the binding of U1 RNP to hnRNP was by protein-protein and/or protein-RNA interactions.     

Unilateral lesions of the hamster suprachiasmatic nuclei: evidence for redundant control of circadian rhythms

Summary Several properties of vertebrate circadian rhythms can be attributed to the behavior of an underlying pacemaker system which is composed of two separate but mutually interacting circadian oscillators. As originally formulated, the model for such a pacemaker system proposed that two oscillators or populations of oscillators have different properties, specifically in their responses to light (Pittendrigh 1974; Pittendrigh and Daan 1976b). We have tested the proposition that the right and left suprachiasmatic nuclei (SCN) of the golden hamster contribute in different ways to the regulation of circadian rhythmicity by measuring the wheel-running activity rhythms of hamsters with lesions to either the right or left SCN. Although effects of unilateral or other partial SCN lesions on pacemaker properties were observed, these effects were not different in hamsters receiving right- or left-side lesions. More specifically: (1) free-running period () in constant light was shorter in lesioned hamsters irrespective of the side lesioned (Fig. 3a), and the total amount of SCN destruction was found to correlate with (Fig. 4). (2) Phase-angle difference () of some lesioned hamsters (both right- and left-side) during entrainment to LD, 1410 was significantly more positive than that of controls (Fig. 3b). (3) The rate of phase-shift following a shift of the light/dark cycle was not different in hamsters with right- or left-side lesions (Fig. 3c). And (4) the simultaneous expression of different circadian periods, similar to splitting, was observed in hamsters with unilateral lesions (Fig. 5). It is concluded that the right and left SCN are similar in their contributions to the control of circadian rhythmicity and that there is as yet no evidence for the permanent loss of multioscillator properties resulting from the destruction of only one of the two SCN.Abbreviations SCN suprachiasmatic nuclei or nucleus - LD light/dark cycle - LL constant light - DD constant dark - circadian period - activity time - rest time - phase angle - phase-angle difference - SD standard deviation - SE standard error - ANOVA analysis of variance     

The polyadenylated RNA of zoospores and growth phase cells of the aquatic fungus,Blastocladiella

The stored poly(A) + RNA from zoospores of the aquatic fungus Blastocladiella emersonii represents 2.5% of the total RNA and has a model MW of 425,000 daltons and an average poly(A) isostich of 32 bases. The poly(A) + RNA also represents 2.5% of the total RNA from early growth phase cells and has a modal MW of 360,000 daltons and an average poly(A) isostich of 38 bases. The poly(A) + RNA from spores and 2-hr plants contains a structure resistant to RNases T₁, T₂, and A, which can be labeled with ³²PO₄ and which will bind to DBAE-cellulose. These characteristics strongly suggest that both the zoospore poly(A) + RNA and the 2-hr cell poly(A) + RNA are capped at the 5′ end; and, hence, it is unlikely that capping is involved in the control of protein synthesis during germination.Approximately 80% of the poly(A) + RNA of the spore is located in the membrane-enclosed ribosomal nuclear cap, and more than 90% of the poly(A) + RNA within the cap is found in the 80S monoribosome and heavier fractions.Synthesis of new poly(A) + RNA occurs very early during zoospore germination, and the labeled poly(A) + RNA rapidly enters the newly organized polysomes. The labeling data for early germination also suggest that cytoplasmic polyadenylation occurs.     

β-endorphin proteolysis by guinea-pig ileum myenteric plexus membranes: Increased γ-endorphin turnover after chronic exposure to morphine

The influence of chronic morphine exposure $\text{in vitro}$ on the biotransformation of β-endorphin (βE) was investigated using the myenteric plexus-longitudinal muscle of guinea-pig ileum. A membrane preparation was incubated with βE and the degradation of βE as well as the accumulation of several βE fragments in the incubation medium were followed with time. The levels of peptides were determined by specific radioimmunoassays after separation by high-pressure liquid chromatography. It was found that exposure to morphine did not affect the disappearance of βE, but altered the time course of accumulation of βE fragments. In fact, the accumulation of γ-endorphin, α-endorphin and des-tyrosine¹-α-endorphin was enhanced, while that of des-tyrosine¹-γ-endorphin was not changed. Additionally, the disappearance of γ-endorphin appeared to be stimulated by morphine exposure. These data provide evidence that the fragmentation of βE is changed by chronic morphine exposure in such a way that the turn-over of γ-endorphin is increased.     

Ingenol esters from the pro-inflammatory fraction of Euphorbia kamerunica

A series of unstable mono- and di-esters of the tetracyclic diterpene ingenol were isolated from the pro-inflammatory ether-soluble fraction of the latex of Euphorbia kamerunica. The esters were isolated by a neutral process involving column and thin-layer chromatography. The monoesters were identified by spectroscopic methods and hydrolysis reactions as ingenol-3-decanoate, ingenol-3-dodecanoate, ingenol-5-hexadienoate and ingenol-5-octenoate and the diesters as 20-acetyl-ingenol-3-octenoate and 20-acetyl-ingenol-3-angelate.