Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex?

Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R-6 distance-dependent Förster rate expression. However, such interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen and human serum albumin (HSA), as well as a model flurbiprofen-Trp dyad, in which recent observations of enantioselective fluorescence quenching has been ascribed to energy transfer from flurbiprofen to Trp. To this aim, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics (QM/MM) calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement among theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S)- and (R)- enantiomers of flurbiprofen. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-flurbiprofen enantiomer in the binding pocket

post hoc analysis of the effect of baseline characteristics on treatment duration in patients with metastatic castration resistant prostate cancer mcrpc receiving cabazitaxel in the compassionate use cup expanded access programs eap and capristana registry

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Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations

The IEFPCM/MST continuum solvation model is used for the blind prediction of n-octanol/water partition of a set of 11 fragment-like small molecules within the SAMPL6 Part II Partition Coefficient Challenge. The partition coefficient of the neutral species (log P) was determined using an extended parametrization of the B3LYP/6-31G(d) version of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol. Comparison with the experimental data provided for partition coefficients yielded a root-mean square error (rmse) of 0.78 (log P units), which agrees with the accuracy reported for our method (rmse = 0.80) for nitrogen-containing heterocyclic compounds. Out of the 91 sets of log P values submitted by the participants, our submission is within those with an rmse < 1 and among the four best ranked physical methods. The largest errors involve three compounds: two with the largest positive deviations (SM13 and SM08), and one with the largest negative deviations (SM15). Here we report the potentiometric determination of the log P for SM13, leading to a value of 3.62 ± 0.02, which is in better agreement with most empirical predictions than the experimental value reported in SAMPL6. In addition, further inclusion of several conformations for SM08 significantly improved our results. Inclusion of these refinements led to an overall error of 0.51 (log P units), which supports the reliability of the IEFPCM/MST model for predicting the partitioning of neutral compounds

Carbon Nanotubes by a CVD Method. Part I: Synthesis and Characterization of the (Mg, Fe)O Catalysts

The controlled synthesis of carbon nanotubes by chemical vapor deposition requires tailored and wellcharacterized catalyst materials. We attempted to synthesize Mg1-xFexO oxide solid solutions by the combustion route, with the aim of performing a detailed investigation of the influence of the synthesis conditions (nitrate/urea ratio and the iron content) on the valency and distribution of the iron ions and phases. Notably, characterization of the catalyst materials is performed using 57Fe Mo¨ssbauer spectroscopy, X-ray diffraction, and electron microscopy. Several iron species are detected including Fe2+ ions substituting for Mg2+ in the MgO lattice, Fe3+ ions dispersed in the octahedral sites of MgO, different clusters of Fe3+ ions, and MgFe2O4-like nanoparticles. The dispersion of these species and the microstructure of the oxides are discussed. Powders markedly different from one another that may serve as model systems for further study are identified. The formation of carbon nanotubes upon reduction in a H2/CH4 gas atmosphere of the selected powders is reported in a companion paper

Structural and energetic study of cation-p-cation interactions in proteins

Cation-pi interactions of aromatic rings and positively charged groups are among the most important interactions in structural biology. The role and energetic characteristics of these interactions are well established. However, the occurrence of cation-pi-cation interactions is an unexpected motif, which raises intriguing questions about its functional role in proteins. We present a statistical analysis of the occurrence, composition and geometrical preferences of cation-pi-cation interactions identified in a set of non-redundant protein structures taken from the Protein Data Bank. Our results demonstrate that this structural motif is observed at a small, albeit non-negligible frequency in proteins, and suggest a preference to establish cation-pi-cation motifs with Trp, followed by Tyr and Phe. Furthermore, we have found that cation-pi-cation interactions tend to be highly conserved, which supports their structural or functional role. Finally, we have performed an energetic analysis of a representative subset of cation-pi-cation complexes combining quantum-chemical and continuum solvation calculations. Our results point out that the protein environment can strongly screen the cation-cation repulsion, leading to an attractive interaction in 64% of the complexes analyzed. Together with the high degree of conservation observed, these results suggest a potential stabilizing role in the protein fold, as demonstrated recently for a miniature protein (Craven et al., J. Am. Chem. Soc. 2016, 138, 1543). From a computational point of view, the significant contribution of non-additive three-body terms challenges the suitability of standard additive force fields for describing cation-p-cation motifs in molecular simulations. Keywords: Cation-π−cation complexes; noncovalent interactions; cooperativity; protein structure

Open Peer Review Module (OPRM). Final Report

Research productivity is increasing at an unprecedented rate. Technological innovations, a surge in available computing power, and the ease with which digital information is stored and communicated is helping researchers to cross experimentation boundaries, to increase data availability, and to facilitate the transfer of knowledge. As a result, traditional research is being transformed into a dynamic and globally interconnected effort where ideas, tools and results can be made instantly accessible to the entire academic community. Institutional and multidisciplinary open access repositories play a crucial role in this emerging landscape by enabling immediate accessibility to all kinds of research output. One important element still missing from open access repositories, however, is a quantitative assessment of the hosted research items that will facilitate the process of selecting the most relevant and distinguished content. Common currently available metrics, such as number of visits and downloads, do not reflect the quality of a research work, which can only be assessed directly by peers offering their expert opinion together with quantitative ratings based on specific criteria. To address this issue we developed an Open Peer Review Module (OPRM) to be installed on existing open access repositories and offered as an overlay service. Any digital research work hosted in a compliant repository can then be evaluated by an unlimited number of peers who offer not only a qualitative assessment in the form of text, but also quantitative measures that are used to build the reputation of the research work and its authors. Crucially, this evaluation system is open and transparent. By open we mean that the full text of the peer reviews are publicly available along with the original research work. By transparent we mean that the identity of the reviewers is disclosed to the authors and to the public. In our model, openness and transparency are two elemental aspects we consider necessary to address the issue of biased or non-expert opinions, which is inherent in the anonymous peer review model, characterized by the unaccountability of reviewers. Importantly, our open peer review module includes a reviewer reputation system based on the assessment of reviews themselves by other peer reviewers. This allows a sophisticated scaling of the importance of each review on the overall assessment of a research work, based on the reputation of the reviewer. The implementation of a peer review layer on top of institutional repositories could have the potential to transform the current academic publication landscape by introducing new scholarly workflows where a research item can be openly evaluated by the world’s experts right at the institutional repository of its authors, before being submitted to an academic journal. This workflow challenges the current practices of peer review research evaluation. In most cases, journals, acting as brands in a competitive market, foster academic competition for a limited number of publication slots, instead of promoting open scholarship and collaboration. The integration of peer review in repositories will enable direct and transparent academic collaboration between authors and reviewers. In addition, the use of the OPRM will produce novel metrics directly reflecting the perceived quality of a research work by expert peers, contrary to current available altmetrics that only indirectly account for quality through usage statistics.OpenAIR

Intravenous Cyclophosphamide Pulse Therapy in the Treatment of Systemic Sclerosis-Related Interstitial Lung Disease: A Long Term Study

Interstitial lung disease (ILD) frequently complicates systemic sclerosis (SSc). Cyclophosphamide (CYC) is a promising immunosuppressive therapy for SSc-related ILD. Our objective was to investigate the effectiveness of an intravenous CYC (iv CYC) pulse regime in SSc-related ILD during treatment and thereafter. In a prospective observational study ten consecutive patients with SSc-related ILD were treated with iv CYC in a pulse regime lasting from 6 to 24 months. Clinical status, pulmonary functional testing (PFT) and high resolution computed tomography (HRCT) of the chest were evaluated at enrolment and 6, 12 and 24 months thereafter. After treatment withdrawal, patients were followed up every 6 months with PFT and chest HRCT to monitor lung disease. Clinical improvement was apparent in 8 out of 10 patients. The median values of forced vital capacity (FVC), forced expiratory volume in the first second (FEV1) and diffusion lung capacity for carbon monoxide (DLCO) as well as ground-glass pattern on HRCT did not change significantly after 6, 12 and 24 months of therapy. The follow-up continued in 8 out of 10 patients after treatment withdrawal for a median of 26.5 months (range: 12-48 months). The final median FVC was 54.5% of predicted value (interquartile range, IQR= 31.6%-94%). Only one patient suffered a FVC deterioration greater than 10%, even though less than 160 ml. The final median DLCO was 68% of predicted value (IQR=38.3-83.6%). Only 2 patients who developed pulmonary arterial hypertension deteriorated their DLCO values of more than 15%. An iv CYC pulse regimen over 24 months may stabilize pulmonary activity in patients with SSc-related ILD during the course of treatment and for a median of 26.5 months thereafter

Does ALS-FUS without FUS mutation represent ALS-FET? Report of three cases

Altres ajuts: This study was partially funded by Fundacio Marató de TV3 (grant no. 20143810 to RSV, no. 20141610 to EG and no. 201437.10 to RRG) and Fondo Europeo de Desarrollo Regional (FEDER) (PI16/01673 to JG and PI15/01618 to RRG). We are indebted to the Neurological Tissue Bank of the Biobanc-Hospital Clinic-IDIBAPS, Barcelona, Spain, for data and sample procurement. We thank Sara Charif, Veronica Santiago, Carmen Schweiger, Leire Etxarri and Abel Muñoz for technical assistance

Tracking Asian tiger mosquito introductions in the Netherlands using Nextstrain

The Asian tiger mosquito Aedes albopictus is an undesirable invasive mosquito species that causes considerable nuisance through its biting behaviour, and has been proven to transmit more than 22 different viruses under laboratory conditions. Human-aided transportation, the capacity of winter diapause, and possibly global warming have contributed to the global invasion of Ae. albopictus. The species was found for the first time in the Netherlands in 2005, and since 2010 has been found introduced at many locations throughout the country. Elucidating the origin of these introduced mosquitoes could help the authorities on the planning and evaluation of the risk-based surveillance of Aedes invasive mosquitoes. This study aims to determine the genomic diversity of Ae. albopictus that is represented within and between collection sites with a database consisting of Ae. albopictus specimens from past introductions in the Netherlands, specimens from populations from other regions in the world, and data from specimens present in databases. In this study, complete mitochondrial genomes were sequenced, a recommended marker for phylogeography analysis of Ae. albopictus. Metadata is presented in a Nextstrain build containing 254 Ae. albopictus genomes up to October 2020. Overall, the phylogeny results of the Nextstrain build reveals a low mitogenomic diversity within Ae. albopictus. Genomic diversity of Ae. albopictus specimens found in the Netherlands fall within one main cluster which is hypothesised to represent the globally invasive strain of the species. Other organisations are stimulated to share data or materials for inclusion and improvement of the Nextstrain build, which can be accessed at https://nextstrain.nrcnvwa.nl/Aedes/20210728.info:eu-repo/semantics/publishedVersio

Dating of the hominid (Homo neanderthalensis) remains accumulation from El Sidrón Cave (Piloña, Asturias, North Spain): an example of a multi-methodological approach to the dating of Upper Pleistocene sites.

The age of Neanderthal remains and associated sediments from El Sidrón cave has been obtained through different dating methods (14CAMS, U/TH, OSL, ESR and AAR) and samples (charcoal debris, bone, tooth dentine, stalagmitic flowstone, carbonate-rich sediments, sedi- mentary quartz grains, tooth enamel and land snail shells). Detrital Th contamination ren- dered Th/U dating analyses of flowstone unreliable. Recent 14C contamination produced spurious age-values from charcoal samples as well as from inadequately pretreated tooth samples. Most consistent 14C dates are grouped into two series: one between 35 and 40 ka and the other between 48 and 49 ka. Most ESR and AAR samples yielded concordant ages, ranging between 39 and 45 ka; OSL dating results permitted adequate bracketing of the sedimentary layer that contained the human remains. Our results emphasize the value of multi-dating approaches for the establishment of reliable chronologies of human remains