Benefits versus risks of pharmacological prophylaxis to prevent symptomatic venous thromboembolism in unselected medical patients revisited. Meta-analysis of the medical literature.

A significant proportion of the outcomes reported in trials assessing venous thromboembolism (VTE) prophylaxis in medical patients are related to asymptomatic events found on routine imaging studies. The implications of these events are controversial. Moreover, such trials did not always reflect the patient mix in today's internal medicine departments. We summarized the evidence assessing the rate of symptomatic VTE events and the benefit of pharmacological prophylaxis in unselected medical patients, and formally evaluated the benefit versus risk of this intervention. We searched MEDLINE, EMBASE and CENTRAL until June 2011 for studies that prospectively followed cohorts of medical patients and assessed the rates of VTE, and randomized controlled trials reporting the effect of prophylaxis on these events, at 3 weeks and 3 months. Eight trials were included. The rates of symptomatic VTE were 0.69 and 3.7 % for short term and long term follow-up periods, respectively. In the interventional meta-analysis, the odds ratio (OR) for overall mortality and for symptomatic VTE at 3 weeks were 0.93 and 0.59, favouring intervention. The OR for major bleeding at 3 weeks was 2.0, favouring no intervention. None of these results were statistically significant. The number needed to treat to prevent one overt VTE event was 292, while the number needed to treat for an additional major bleeding was 336. In unselected medical patients, the rate of symptomatic VTE is lower than the reported overall VTE rate, and the benefit to risk ratio of pharmacological intervention for alleviating this condition in at-risk medical inpatient is questionable. Further specifying the population at risk for an overt VTE, and the clinical significance of asymptomatic events, is warranted.

Early structural evolution of native cytochrome c after solvent removal.

Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds; instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations.

The dynamics of water evaporation from partially solvated cytochrome c in the gas phase.

The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the mass spectrometer. In this work the dynamics of water evaporation from native cytochrome c covered by a monolayer of water is studied by molecular dynamics (MD) simulations at constant energy. A model of the initial conditions of the process is introduced. The temperature of the protein drops by about 100 K during the 400 picoseconds of the simulations. This sharp drop in temperature causes the water evaporation rate to decrease by about an order of magnitude, leaving the protein with 50% to 90% of the original water molecules, depending on the initial temperature of the simulation. The structural changes of the protein upon desolvation were considered through calculations of the radius of gyration and the root mean square (RMS) of the protein. A variation of 0.4 A in the radius of gyration, together with an RMS value of less than 3 A, indicates only minor changes in the overall shape of the protein structure. The water coordination number of the solvation shell is much smaller than that for bulk water. The mobility of water is high at the beginning of the simulations and drops as the simulation progresses and the temperature decreases. Incomplete desolvation of protein ions was also observed in recent experiments.

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy.

The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.