Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE.

Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin.

The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Idiopathic (unexplained) pulmonary embolism is associated with an impaired prognosis compared to other entities of pulmonary embolism.

In patients following acute pulmonary embolism, little is known about long-term prognosis attributed to individual risk factors and entities of pulmonary embolism. The aim of our study was to identify predictors of long-term mortality and morbidity, taking into account precipitating causes and entities of pulmonary embolism, especially in cases of idiopathic pulmonary embolism. We reviewed the records of 257 consecutive patients presenting with acute pulmonary embolism in the emergency room of the University Hospital in Frankfurt between 1997 and 2006. The median of the follow-up time in this study population was 670 days (n = 236; interquartile range: 378-1397 days). The patients were divided into three groups depending on the cause of pulmonary embolism: idiopathic pulmonary embolism (n = 83; 33%), neoplasm (n = 44; 17%) and other causes (n = 130; 50%). As expected, patients with neoplastic-associated pulmonary embolism demonstrated the poorest prognosis in the Kaplan-Meier analysis. Surprisingly though, patients with idiopathic pulmonary embolism demonstrated a markedly worse long-term survival compared with other causes (log-rank P < 0.001). When Cox-regression analysis was restricted to patients discharged alive without neoplasm, idiopathic pulmonary embolism was the strongest predictor of long-term mortality (hazard ratio: 3.29; P = 0.017). Patients with acute pulmonary embolism and known malignancy demonstrated the highest mortality compared with those with other causes. However, idiopathic pulmonary embolism is a common diagnosis and is associated with an unfavorable long-term prognosis compared with other entities of pulmonary embolism.

Rostro-caudal gradual loss of cellular diversity within the periventricular regions of the ventricular system.

Neurogenesis occurs constitutively within the periventricular region (PVR) of the lateral ventricles (LV) of the adult mammalian brain. The occurrence of adult neurogenesis within the PVR outside the neurogenic niche of the LV remains controversial, but neural stem cells can be isolated from PVR of the whole ventricular system. The histological basis of this phenomenon including the regional differences of cellular phenotypes within the PVRs is still enigmatic. The occurrence of neurogenesis or manipulable progenitor cells in caudal parts of the adult brain is however one prerequisite for orthotopic regenerative approaches in Parkinson's disease (PD) and other disorders of the midbrain/brainstem. Using quantitative immunohistochemical techniques and electron microscopy, we found a rostro-caudal gradual loss of cellular diversity within the PVR throughout the whole ventricular axis with loss of transit amplifying epidermal growth factor-receptor(+) type C cells in all parts caudal to the LV, a gradual reduction from rostral to caudal of both stem cells (type B cells or astrocytes) without signs of proliferation outside the PVR of the LV as well as neuroblasts-like cells (polysialylated neural cell adhesion molecule [PSA-NCAM](+), but doublecortin negative cells) with a different morphology compared with neuroblasts of the PVR of the LV. Electron microscopy confirmed these immunohistochemical data. The proportion of Nestin(+)/CD24(+) cells and Nestin(+)/S100beta(+) ependymal cells were consecutively increased in the PVR from rostral to caudal, and ultrastructural analysis showed a region-specific morphology with darker cytoplasm with occasional large lipid droplets as well as indented nuclei within the caudal PVRs. The strong correlation of neuroblast-like cells with the number of neurosphere-forming cells suggests that a quiescent subtype of PSA-NCAM(+) cells might be a source of neurosphere-forming cells. We did not find any evidence for neurogenesis or the occurrence of neuroprogenitors within the substantia nigra or other parts of the midbrain/brainstem outside the PVR. Our data provide the histological framework for future studies on orthotopic regenerative approaches in PD by recruiting endogenous predopaminergic progenitors from the midbrain PVR.

Incidence, clinical characteristics, and long-term prognosis of travel-associated pulmonary embolism.

AIMS: Prolonged air travel is considered a risk factor for pulmonary embolism (PE). The clinical characteristics as well as the long-term prognosis of patients suffering from travel-associated PE ('economy-class syndrome', ECS) remain largely unknown. Owing to its proximity, our hospital is the primary referral centre for Frankfurt Airport, Europe's third-largest airport. The goal of our study was to follow-up all patients with ECS, who were admitted to our hospital between 1997 and 2006. METHODS AND RESULTS: We systematically reviewed all medical charts from patients presenting with acute PE to our emergency room or intensive care unit (ICU) and performed a telephone follow-up on patients discharged alive. Together with the data provided from the statistics department of Fraport Inc., the operating company of the Frankfurt International Airport, we were also able to put the medical data in context with the corresponding number of passengers and flight distances. A total of 257 patients with acute PE were admitted to our emergency and ICU between 1997 and 2006. Out of these, 62 patients suffered from ECS (45 flight-associated PE and 17 from other travel-associated PE). ECS patients were prone to more haemodynamic relevant acute events, reflected by a higher rate of initial cardiopulmonary resuscitation (4.8% vs. 1.5%; P = 0.153) and higher percentage of massive PE (8% vs. 3%; P = 0.064). Nevertheless, intrahospital mortality was similar in both groups (ECS 4.8%, others 4.1%; P = 0.730). Interestingly, the long-term outcome of ECS patients was excellent (Kaplan-Meier analysis; P log-rank: 0.008 vs. other entities). In general, ECS was a rare event (one event/5 million passengers), where long-haul flights over 5000 km lead to a 17-fold risk increase compared with shorter flights. CONCLUSIONS: Travel-associated PE was a common cause of PE in our hospital, with patients showing excellent long-term prognosis after discharge. The risk of ECS is rather low and strictly dependent on the flight distance.

Vibronic coupling in the ground and excited states of oligoacene cations.

The vibrational coupling in the ground and excited states of positively charged naphthalene, anthracene, tetracene, and pentacene molecules is studied on the basis of a joint experimental and theoretical study of ionization spectra using high-resolution gas-phase photoelectron spectroscopy and first-principles correlated quantum-mechanical calculations. Our theoretical and experimental results reveal that, while the main contribution to relaxation energy in the ground state of oligoacene systems comes from high-energy vibrations, the excited-state relaxation energies show a significant redistribution toward lower-frequency vibrations. A direct correlation is found between the nature of the vibronic interaction and the pattern of the electronic state structure.

Lithium intercalation of phenyl-capped aniline dimers: a study by photoelectron spectroscopy and quantum chemical calculations.

Structural and electronic properties of pristine and lithium-intercalated, phenyl-capped aniline dimers as a model for the lithium-polyaniline system have been studied by photoelectron spectroscopy and quantum chemical calculations. It was found that the electronic structure of reduced and oxidized forms of oligoanilines is only weakly affected by isomerism. Upon intercalation, charge transfer from the Li-atoms is remarkable and highly localized at N-atomic sites, where configurations are energetically favored in which both N atoms of the dimers are bound to Li atoms. Conversion of nitrogen sites is different for the two forms of aniline dimers and incomplete up to high intercalation levels, indicating a pronounced role of solid-state effects in the formation of such compounds.

Vibronic coupling in the ground and excited states of the naphthalene cation.

The hole-vibrational coupling in naphthalene is studied using high-resolution gas-phase photoelectron spectroscopy and density functional theory calculations (DFT), and a remarkable increase of the coupling with low-frequency vibrations is observed in the excited states.