Ab-Initio Fragment Method for Calculating Molecular X-ray Diffraction

A fragment-based approach for the prediction of elastic X-ray scattering is presented. The total diffraction pattern is assembled from anisotropic form factors calculated for individual molecular fragments, optionally including corrections for pairwise interactions between fragments. The approach is evaluated against full ab initio scattering calculations in the peptide diphenylalanine, and the optimal selection of fragments is examined in the ethanol molecule. The approach is found to improve significantly on the independent atom model while remaining conceptually simple and computationally efficient. It is expected to be particularly useful for macromolecules with repeated subunits, such as peptides, proteins, DNA, or RNA and other polymers, where it is straightforward to define appropriate fragments

Ab initio molecular diffraction

In 1915, Debye derived his well-known equation for the X-ray scattering from a sample of randomly orientated gas-phase molecules. He approximated the molecular scattering by adding the contributions of isolated atomic constituents. This is known as the Independent Atom Model (IAM). However, it omits the redistribution of valence electrons due to bonding, and is limited to the electronic ground state. The main proposition of this thesis is that it is worthwhile going beyond the IAM when interpreting X-ray scattering data. In part, this is motivated by the arrival of new X-ray sources called X-ray Free-Electron Lasers (XFELs). A new method called Ab Initio X-ray Diffraction (AIXRD) is introduced. It calculates the elastic X-ray molecular scattering factor directly from wave functions calculated by ab initio electronic structure theory, for instance Hartree-Fock or multiconfigurational self-consistent field. In this way, the valence electrons are correctly taken into account, and calculations based on electronically excited wave functions become possible. The wave functions must be constructed from spatial orbitals made up of Gaussian-Type Orbitals (GTOs), giving an analytical solution to the Fourier transform integrals involved, and is key to computationally efficient and accurate results. This is compared to a fast Fourier transform (FFT) method, where the electron density is computed on a 3D grid and an FFT algorithm is used to obtain the elastic X-ray molecular scattering factor. Inspired by post-crystallography experiments such as serial femtosecond crystallography and single-particle imaging at XFELs, the AIXRD method is expanded to allow accurate X-ray diffraction calculations from large molecules such as proteins. To make the underlying ab initio problem tractable, the molecule is split into fragments. In other words, the electron density is constructed by a sum of fragment contributions, as is the corresponding molecular form-factor. In this way, it is analogous to the IAM approach except that instead of isolated atoms, there are isolated fragments. A pairwise summation of fragment contributions is also used to account for fragment-fragment interactions. Various fragment definitions are compared based on their effect on the X-ray diffraction signal, and are compared to the IAM method. Finally, X-ray diffraction from molecules in specific quantum states is calculated, revealing a distinct quantum fingerprint in the X-ray diffraction, and a comparison to experiment is made. In particular, the elastic X-ray diffraction is calculated from gas-phase H2 pumped to various electronic, vibrational, and electronic states. This is expanded upon for polyatomic molecules using the harmonic approximation for the vibrational states

Elastic X-ray scattering from state-selected molecules

International audienceThe characterization of electronic, vibrational, and rotational states using elastic (coherent) X-ray scattering is considered. The scattering is calculated directly from complete active space self-consistent field level ab initio wavefunctions for H-2 molecules in the ground-state X-1 Sigma(+)(g) and first-excited EF1 Sigma(+)(g) electronic states. The calculated scattering is compared to recent experimental measurements [Y.-W. Liu et al., Phys. Rev. A 89, 014502 (2014)], and the influence of vibrational and rotational states on the observed signal is examined. The scaling of the scattering calculations with basis set is quantified, and it is found that energy convergence of the ab initio calculations is a good indicator of the quality of the scattering calculations. Published by AIP Publishing

IntPred: a structure-based predictor of protein–protein interaction sites

Motivation Protein–protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein– protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein–protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods. Results On an independent test set of obligate and transient complexes, our IntPred predictor performs well (MCC = 0.370, ACC = 0.811, SPEC = 0.916, SENS = 0.411) and compares favourably with other methods. Overall, IntPred ranks second of six methods tested with SPPIDER having slightly better overall performance (MCC = 0.410, ACC = 0.759, SPEC = 0.783, SENS = 0.676), but considerably worse specificity than IntPred. As with SPPIDER, using an independent test set of obligate complexes enhanced performance (MCC = 0.381) while performance is somewhat reduced on a dataset of transient complexes (MCC = 0.303). The trade-off between sensitivity and specificity compared with SPPIDER suggests that the choice of the appropriate tool is application-dependent. Availability and implementation IntPred is implemented in Perl and may be downloaded for local use or run via a web server at www.bioinf.org.uk/intpred/. Supplementary information Supplementary data are available at Bioinformatics online

The contributions of molecular vibrations and higher triplet levels to the intersystem crossing mechanism in metal-free organic emitters.

Intense, simultaneous, room temperature phosphorescence (RTP) and thermally activated delayed fluorescence (TADF) is observed in a series of donor-acceptor-donor (D–A–D) molecules. This dual-luminescence is stronger in the “angular” isomers, compared to their “linear” regioisomers, which is consistent with an enhanced intersystem crossing (ISC) in the former. Herein, we demonstrate that the small energy gap between the triplet levels, T1-Tn, below the lowest singlet state, S1, in the “angular” regioisomers, enhances the coupling between S1 and T1 states and favors ISC and reverse ISC (rISC). This is consistent with a spin-vibronic mechanism. In the absence of this “triplet ladder”, due to the larger energy difference between T1 and Tn in the “linear” regioisomers, the ISC and rISC are not efficient. Remarkably the enhancement on the ISC rate in the “angular” regioisomers is accompanied by an increase on the rate of internal conversion (IC). These results highlight the contributions of higher triplet excited states and molecular vibronic coupling to harvest triplet states in organic compounds, and casts the TADF and RTP mechanisms into a common conceptual framework

Transition states in protein folding kinetics: Modeling Phi-values of small beta-sheet proteins

Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Phi-values for two small beta-sheet proteins, the PIN and the FBP WW domain. The native structure of these WW domains comprises two beta-hairpins that form a three-stranded beta-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in Molecular Dynamics folding-unfolding simulations of a small designed three-stranded beta-sheet protein. We obtain good agreement with the experimental data (i) by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins, and (ii) by fitting a single parameter, the relative degree to which hairpin 1 and 2 are formed in the transition state. The model helps to understand how mutations affect the folding kinetics of WW domains, and captures also negative Phi-values that have been difficult to interpret.Comment: 27 pages, 6 pages, 3 tables; to appear in Biophys.

Sentinel surveillance for travellers' diarrhoea in primary care

<p>Abstract</p> <p>Background</p> <p>Travellers' diarrhoea is the most common health problem among international travellers and much of the burden falls on general practitioners. We assessed whether sentinel surveillance based in primary care could be used to monitor changes in the epidemiology of travellers' diarrhoea.</p> <p>Methods</p> <p>A sentinel surveillance scheme of 30 volunteer general practices distributed throughout Wales provides weekly reports of consultations for eight infectious diseases to the national Communicable Disease Surveillance Centre. Travellers' diarrhoea was introduced as a new reportable infection in July 2002.</p> <p>Results</p> <p>Between 1 July 2002 and 31 March 2005 there were 90 reports of travellers' diarrhoea. The mean annual consultation rate was 15.2 per 100,000 population (95% confidence interval: 12.2–18.7), with the highest rates in summer, in people aged 15–24 years, and in travellers to Southern Europe. A higher proportion of travellers than expected had visited destinations outside Europe and North America when compared to the proportion of all United Kingdom travellers visiting these destinations (38% vs. 11%; Chi²= 53.3, p < 0.0001).</p> <p>Conclusion</p> <p>Sentinel surveillance has the potential to monitor secular trends in travellers' diarrhoea and to help characterise population groups or travel destinations associated with higher risk.</p

Generation of Priority Research Questions to Inform Conservation Policy and Management at a National Level

Integrating knowledge from across the natural and social sciences is necessary to effectively address societal tradeoffs between human use of biological diversity and its preservation. Collaborative processes can change the ways decision makers think about scientific evidence, enhance levels of mutual trust and credibility, and advance the conservation policy discourse. Canada has responsibility for a large fraction of some major ecosystems, such as boreal forests, Arctic tundra, wetlands, and temperate and Arctic oceans. Stressors to biological diversity within these ecosystems arise from activities of the country's resource-based economy, as well as external drivers of environmental change. Effective management is complicated by incongruence between ecological and political boundaries and conflicting perspectives on social and economic goals. Many knowledge gaps about stressors and their management might be reduced through targeted, timely research. We identify 40 questions that, if addressed or answered, would advance research that has a high probability of supporting development of effective policies and management strategies for species, ecosystems, and ecological processes in Canada. A total of 396 candidate questions drawn from natural and social science disciplines were contributed by individuals with diverse organizational affiliations. These were collaboratively winnowed to 40 by our team of collaborators. The questions emphasize understanding ecosystems, the effects and mitigation of climate change, coordinating governance and management efforts across multiple jurisdictions, and examining relations between conservation policy and the social and economic well-being of Aboriginal peoples. The questions we identified provide potential links between evidence from the conservation sciences and formulation of policies for conservation and resource management. Our collaborative process of communication and engagement between scientists and decision makers for generating and prioritizing research questions at a national level could be a model for similar efforts beyond Canada

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700