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The European Space Agency's Rosetta spacecraft, with the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) onboard, has been following and observing comet 67P/Churyumov-Gerasimenko since summer 2014. Prior to this period, and due to a technical failure also during this period, optimization and calibration campaigns have been conducted on ground with the Reflectron-type Time Of Flight (RTOF) mass spectrometer as a preparatory work for the analysis of data recorded during the science phase of the mission. In this work, we show the evolution of the performance of RTOF, and demonstrate and quantify the sensitivity and functionality of RTOF onboard Rosetta. We also present a fragmentation and sensitivity database for the most abundant molecules observed around the comet such as H 2 O, CO, CO 2 , as well as the noble gases. [ABSTRACT FROM AUTHOR]

ABSTRACT Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo-chemically strained. Here, we present a fully automated algorithm, called AbPredict, that disregards sequence homology, and instead uses a Monte Carlo search for low-energy conformations built from backbone segments and rigid-body orientations that appear in antibody molecular structures. We find cases where AbPredict selects accurate loop templates with sequence identity as low as 10%, whereas the template of highest sequence identity diverges substantially from the query's conformation. Accordingly, in several cases reported in the recent Antibody Modeling Assessment benchmark, AbPredict models were more accurate than those from any participant, and the models' stereo-chemical quality was consistently high. Furthermore, in two blind cases provided to us by crystallographers prior to structure determination, the method achieved <1.5 Ångstrom overall backbone accuracy. Accurate modeling of unstrained antibody structures will enable design and engineering of improved binders for biomedical research directly from sequence. Proteins 2016; 85:30-38. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The tremendous pandemic potential of coronaviruses was demonstrated twice in the last 15 years by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. Despite their biomedical importance, coronavirus S glycoproteins have proven difficult targets for structural characterization, precluding high-resolution studies of the biologically relevant trimer. Recent technological developments in single particle cryo-electron microscopy allowed us to determine the first structure of a coronavirus S glycoprotein trimer which provided a framework to understand the mechanisms of viral entry and suggested potential inhibition strategies for this family of viruses. Here, we describe the key factors that enabled this breakthrough. [ABSTRACT FROM AUTHOR]

Armadillo repeat proteins (ArmRPs) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. Thus, they may form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library. Stacked armadillo repeats, each consisting of 42 aa arranged in three α-helices, build an elongated superhelical structure. Here, we analyzed the curvature variations in natural ArmRPs and identified a repeat pair from yeast importin-α as having the optimal curvature geometry that is complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry. Computationally designed ArmRPs (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series. [ABSTRACT FROM AUTHOR]

Die Rosetta-Mission ist ein Meilenstein in der Erforschung der Kometen und ihrer Entstehung. Eine der größten Überraschungen war die unregelmäßige hantelförmige Gestalt des Zielkometen 67P/Tschurjumow-Gerassimenko. Er besteht wahrscheinlich aus zwei Einzelkörpern, die durch ihre Schwerkraft aneinander gehalten werden. Seine Oberfläche ist sehr rau und zeigt eine sehr vielfältige Morphologie, die auf eine Vielzahl von ablaufenden Prozessen hindeutet. Der Kometenkern ist vermutlich auf Größenskalen von mehr als etwa 10 bis 100 Metern homogen, Inhomogenitäten auf kleineren Skalen könnten für seine Aktivität verantwortlich sein. Diese ist auf kleine Gebiete konzentriert, und auch Oberflächenveränderungen, die sich innerhalb von einigen Tagen bis wenigen Wochen abspielen, sind lokal. Im Kometenmaterial wurde eine Vielzahl an organischen Substanzen gemessen, die zum Teil als Schlüsselmoleküle für die Synthese der Grundbausteine des Lebens gelten, wie wir es kennen. [ABSTRACT FROM AUTHOR]

Recombinant protein production is at the core of biotechnology and numerous molecular tools and bacterial strains have been developed to make the process more efficient. One commonly used generic solution is to supply extra copies of low-abundance tRNAs to compensate for the presence of complementary rare codons in genes-of-interest. Here we show that such extra tRNA, supplied by the commonly used pLysSRARE2 plasmid, can cause two side effects: (1) growth and gene expression can be impaired, and (2) apparent positive effects can be caused by differential expression of the lysozyme gene encoded on the same plasmid and not the tRNAs per se. These phenomena seem to have been largely overlooked despite the huge popularity of the T7/pET-based systems for bacterial protein production. [ABSTRACT FROM AUTHOR]

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. [ABSTRACT FROM AUTHOR]

ABSTRACT In his 1875 monograph on insectivorous plants, Darwin described the feeding reactions of Drosera flypaper traps and predicted that their secretions contained a 'ferment' similar to mammalian pepsin, an aspartic protease. Here we report a high-quality draft genome sequence for the cape sundew, Drosera capensis, the first genome of a carnivorous plant from order Caryophyllales, which also includes the Venus flytrap ( Dionaea) and the tropical pitcher plants ( Nepenthes). This species was selected in part for its hardiness and ease of cultivation, making it an excellent model organism for further investigations of plant carnivory. Analysis of predicted protein sequences yields genes encoding proteases homologous to those found in other plants, some of which display sequence and structural features that suggest novel functionalities. Because the sequence similarity to proteins of known structure is in most cases too low for traditional homology modeling, 3D structures of representative proteases are predicted using comparative modeling with all-atom refinement. Although the overall folds and active residues for these proteins are conserved, we find structural and sequence differences consistent with a diversity of substrate recognition patterns. Finally, we predict differences in substrate specificities using in silico experiments, providing targets for structure/function studies of novel enzymes with biological and technological significance. Proteins 2016; 84:1517-1533. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The cover image, by Rachel W. Martin et al., is based on the Article Novel proteases from the genome of the carnivorous plant Drosera capensis: structural prediction and comparative analysis, DOI: 10.1002/prot.25095. [ABSTRACT FROM AUTHOR]

The International Rosetta Mission was launched on 2nd March 2004 on its 10 year journey to rendezvous with comet 67P Churyumov-Gerasimenko. Rosetta performed comet orbit insertion on the 6th of August 2014, after which it characterised the nucleus and orbited it at altitudes as low as a few kilometres. In November 2014 Rosetta delivered the lander Philae to perform the first soft landing ever on the surface of a comet. The critical landing operations have been conducted with remarkable accuracy and will constitute one of the most important achievements in the history of spaceflight. After this critical operation, Rosetta began the escort phase of the comet in its journey in the Solar System heading to the perihelion, reached in August 2015. Throughout this period, the comet environment kept changing with increasing gas and dust emissions. A first phase of bound orbits was followed by a sequence of complex flyby segments which allowed the scientific instruments to perform in depth investigation of the comet environment and nucleus. The unpredictable nature of the comet activity forced the mission control team to implement unplanned changes to the flight plan prepared for this mission phase and to plan the whole mission in a more dynamic way than originally conceived. This paper describes the details of the landing operations and of the main comet escort phase. It also includes the mission status as achieved after perihelion and the findings about the evolution of the comet and its environment from a mission operations point of view. The lessons learned from this unique and complex operations phase and the plans for the next mission phases, which include a mission extension into 2016, are also described. [ABSTRACT FROM AUTHOR]

Rosetta is the first space mission to rendezvous with a comet. The spacecraft encountered its target 67P/Churyumov-Gerasimenko in 2014 and currently escorts the comet through a complete activity cycle during perihelion passage. The Rosetta Science Ground Segment (RSGS) is in charge of planning and coordinating the observations carried out by the scientific instruments on board the Rosetta spacecraft. We describe the data processing system implemented at the RSGS in order to support data analysis and science operations planning. The system automatically retrieves and processes telemetry data in near real-time. The generated products include spacecraft and instrument housekeeping parameters, scientific data for some instruments, and derived quantities. Based on spacecraft and comet trajectory information a series of geometric variables are calculated in order to assess the conditions for scheduling the observations of the scientific instruments and analyse the respective measurements obtained. Images acquired by the Rosetta Navigation Camera are processed and distributed in near real-time to the instrument team community. A quicklook web-page displaying the images allows the RSGS team to monitor the state of the comet and the correct acquisition and downlink of the images. Consolidated datasets are later delivered to the long-term archive. [ABSTRACT FROM AUTHOR]

In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol. Low resolution models were generated guided by the unambiguous restraints using continuous chain folding for alpha and alpha-beta proteins, and iterative annealing for all beta proteins to take advantage of the strand pairing information implicit in the restraints. The Rosetta fragment/model hybridization protocol was then used to recombine and regularize these models, and refine them in the Rosetta full atom energy function guided by both the unambiguous and the ambiguous restraints. Fifteen out of 19 targets were modeled with GDT-TS quality scores greater than 60 for Model 1, significantly improving upon the non-assisted predictions. Our results suggest that atomic level accuracy is achievable using sparse NOE data when there is at least one correctly assigned NOE for every residue. [ABSTRACT FROM AUTHOR]

We describe CASP11 de novo blind structure predictions made using the Rosetta structure prediction methodology with both automatic and human assisted protocols. Model accuracy was generally improved using coevolution derived residue– residue contact information as restraints during Rosetta conformational sampling and refinement, particularly when the number of sequences in the family was more than three times the length of the protein. The highlight was the human assisted prediction of T0806, a large and topologically complex target with no homologs of known structure, which had unprecedented accuracy—<3.0 A ° root-mean-square deviation (RMSD) from the crystal structure over 223 residues. For this target, we increased the amount of conformational sampling over our fully automated method by employing an iterative hybridization protocol. Our results clearly demonstrate, in a blind prediction scenario, that coevolution derived contacts can considerably increase the accuracy of template-free structure modeling. [ABSTRACT FROM AUTHOR]

The prediction of protein–protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state‐of‐the‐art scoring functions (BACH‐SixthSense, PIE/PISA and Rosetta) in discriminating finite‐temperature ensembles of structures corresponding to the native state and to non‐native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH‐SixthSense and PIE/PISA perform better in distinguishing near‐native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312–1320. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The Rosetta Lander Philae is part of the ESA Rosetta Mission which reached comet 67P/Churyumov–Gerasimenko after a 10 year cruise in August 2014. Since then, Rosetta has been studying both its nucleus and coma with instruments aboard the Orbiter. On November 12th, 2014 the Lander, Philae, was successfully delivered to the surface of the comet and operated for approximately 64 h after separation from the mother spacecraft. Since the active cold gas system aboard the Lander as well as the anchoring harpoons did not work, Philae bounced after the first touch-down at the planned landing site “Agilkia”. At the final landing site, “Abydos”, a modified First Scientific Sequence was performed. Due to the unexpectedly low illumination conditions and a lack of anchoring the sequence had to be adapted in order to minimize risk and maximize the scientific output. All ten instruments could be activated at least once, before Philae went into hibernation. In June 2015, the Lander contacted Rosetta again having survived successfully a long hibernation phase. This paper describes the Lander operations around separation, during descent and on the surface of the comet. We also address the partly successful attempts to re-establish contact with the Lander in June/July, when the internal temperature & power received were sufficient for Philae to become active again. [ABSTRACT FROM AUTHOR]

As part of the European Space Agency׳s ROSETTA Mission the Lander PHILAE touched down on comet 67P/Churyumov–Gerasimenko on November 12, 2014. The magnetic field has been measured onboard the orbiter and the lander. The orbiter׳s tri-axial fluxgate magnetometer RPC-MAG is one of five sensors of the ROSETTA Plasma Consortium. The lander is also equipped with a tri-axial fluxgate magnetometer as part of the ROSETTA Lander Magnetometer and Plasma-Monitor package (ROMAP). This unique setup makes a two point measurement between the two spacecrafts in a relatively small distance of less than 50 km possible. Both magnetometers were switched on during the entire descent, the initial touchdown, the bouncing between the touchdowns and after the final touchdown. We describe a method for attitude determination by correlating magnetic low-frequency waves, which was tested under different conditions and finally used to reconstruct PHILAE׳s attitude during descent and after landing. In these cases the attitude could be determined with an accuracy of better than ± 5 ° . These results were essential not only for PHILAE operations planning but also for the analysis of the obtained scientific data, because nominal sources for this information, like solar panel currents and camera pictures could not provide sufficient information due to the unexpected landing position. [ABSTRACT FROM AUTHOR]

The Micro-Imaging Dust Analysis System (MIDAS) atomic force microscope (AFM) onboard the Rosetta orbiter was the first such instrument launched into space in 2004. Designed only a few years after the technique was invented, MIDAS is currently orbiting comet 67P Churyumov–Gerasimenko and producing the highest resolution 3D images of cometary dust ever made in situ . After more than a year of continuous operation much experience has been gained with this novel instrument. Coupled with operations of the Flight Spare and advances in terrestrial AFM a set of “lessons learned” has been produced, cumulating in recommendations for future spaceborne atomic force microscopes. The majority of the design could be reused as-is, or with incremental upgrades to include more modern components (e.g. the processor). Key additional recommendations are to incorporate an optical microscope to aid the search for particles and image registration, to include a variety of cantilevers (with different spring constants) and a variety of tip geometries. [ABSTRACT FROM AUTHOR]

On the 12th of November 2014, The Rosetta Lander Philae became the first spacecraft to softly land on a comet nucleus. Due to the double failure of the cold gas hold-down thruster and the anchoring harpoons that should have fixed Philae to the surface, it spent approximately two hours bouncing over the comet surface to finally come at rest one km away from its target site. Nevertheless it was operated during the 57 h of its First Science Sequence. The FSS, performed with the two batteries, should have been followed by the Long Term Science Sequence but Philae was in a place not well illuminated and fell into hibernation. Yet, thanks to reducing distance to the Sun and to seasonal effect, it woke up at end of April and on 13th of June it contacted Rosetta again. To achieve this successful landing, an intense preparation work had been carried out mainly between August and November 2014 to select the targeted landing site and define the final landing trajectory. After the landing, the data collected during on-comet operations have been used to assess the final position and orientation of Philae, and to prepare the wake-up. This paper addresses the Flight Dynamics studies done in the scope of this landing preparation from Lander side, in close cooperation with the team at ESA, responsible for Rosetta, as well as for the reconstruction of the bouncing trajectory and orientation of the Lander after touchdown. [ABSTRACT FROM AUTHOR]

On its more than 10 years journey to comet 67P/Churyumov–Gerasimenko, Rosetta carried RadFET ionising dose monitors in the central electronics of the orbiter instrument COSIMA and the lander instrument SESAME. The readings of the dosimeters were corrected for the temperature of the devices during measurements. Because the sensitivity of RadFETs depends on the energy of impinging charged particles, a mean efficiency factor for the prevalent proton radiation was determined by applying nine efficiency models to proton energy spectra of Rosetta's radiation environment. The resulting dose profiles show linear increases of the accumulated dose with time, mainly caused by galactic cosmic radiation, and the arrival of two solar particle events in 2005. The accumulated dose (in Silicon) during 3909 days in space from 2004-03-02 to 2014-11-14 was 3.2 ± 0.6 Gy in case of COSIMA and 1.9 ± 0.4 Gy for SESAME. The deviation of the two measurements is mainly due to the solar particle event in September 2005, which had a 5.3 ± 1.0 times stronger impact on the COSIMA RadFET. Measured dose levels are one order of magnitude lower than those expected before launch for not being exceeded on the 90% confidence level, which is mainly due to the low solar activity during the mission so far. [ABSTRACT FROM AUTHOR]

The Alice far-ultraviolet spectrograph in operation around the comet 67P/Churyumov–Gerasimenko on the Rosetta spacecraft experiences an anomalistic feature (AF) that is ubiquitous at comet separations less than 450 km. This feature is highly temporally variable and displays no relation to any studied parameters with the exception of comet separation. This paper tests several possible causes with simulations and finds that positive ions produce a partial explanation for the anomaly, but still finds no definitive source of the AF. [ABSTRACT FROM AUTHOR]

The Electrical Support System (ESS), which was designed and built in Ireland, handled commands transmitted from the Rosetta spacecraft to the Command and Data Management System (CDMS) aboard its Lander Philae during a ten year Cruise Phase to comet 67P/Churyumov-Gerasimenko as well as at the comet itself. The busy Cruise Phase included three Earth flybys, a fly-by of Mars and visits to two asteroids, Steins and Lutetia. Data originating at the individual Lander experiments measured while en-route to and at the comet were also handled by the ESS which received and reformatted them prior to their transmission by Rosetta to Earth. Since the success of the Lander depended on the acquisition of scientific data, the ESS was defined by the European Space Agency to be Mission Critical Hardware. The electronic design of the ESS and its method of handling communications between the spacecraft and Philae are herein presented. The nominal performance of the ESS during the Cruise Phase and in the course of subsequent surface campaigns is described and the successful fulfilment of the brief of this subsystem to retrieve unique scientific data measured by the instruments of the Philae Lander demonstrated. [ABSTRACT FROM AUTHOR]

Ptolemy is a Gas Chromatograph–Isotope Ratio–Mass Spectrometer (GC–IR–MS) aboard the Philae lander element of the Rosetta mission to comet 67P/Churyumov-Gerasimenko. Developed to determine the chemical and stable light isotopic composition of cometary material, Ptolemy was conceived as a highly flexible instrument able to accommodate changes in operational functionality via software modification. This was considered essential to allow for different modes of operation not only in response to rapid/unexpected changes and opportunities, but also to longer-term shifts in priorities as the overall mission plan (and indeed cometary science in general) changed during the decades from initial concept to landing. Against the backdrop of events of the Philae landing, this paper describes the methods of instrument operation and rational behind them used to achieve the Ptolemy scientific results during the period 12–14th November 2014. In particular we demonstrate the importance of a flexible modular approach to the instrument architecture enabling complex instrument operations, especially in a situation where the environment of exploration is effectively unknown and some of the engineering solutions were being tested in the field for the first time. [ABSTRACT FROM AUTHOR]

The COmet Nucleus Sounding Experiment by Radio wave Transmission (CONSERT / Rosetta) has been designed to sound the interior of the comet 67P/Churyumov-Gerasimenko. This instrument consists of two parts: one onboard Rosetta and the other one onboard Philae. A good CONSERT science measurement sequence requires joint operations of both spacecrafts in a relevant geometry. The geometric constraints to be fulfilled involve the position and the orientation of both Rosetta and Philae. At the moment of planning the post-landing and long-term science operations for Rosetta instruments, the actual comet shape and the landing location remained largely unknown. In addition, the necessity of combining operations of Rosetta spacecraft and Philae spacecraft makes the planning process for CONSERT particularly complex. In this paper, we present the specific methods and tools we developed, in close collaboration with the mission and the science operation teams for both Rosetta and Philae, to identify, rank and plan the operations for CONSERT science measurements. The presented methods could be applied to other missions involving joint operations between two platforms, on a complex shaped object. [ABSTRACT FROM AUTHOR]

The International Rosetta Mission of the European Space Agency (ESA) was launched on 2nd March 2004 on its 10 year journey to comet Churyumov-Gerasimenko and has reached it early August 2014. The main mission objectives were to perform close observations of the comet nucleus throughout its orbit around the Sun and deliver the lander Philae to its surface. This paper describers the activities at mission operations level that allowed the landing of Philae. The landing preparation phase was mainly characterised by the definition of the landing selection process, to which several parties contributed, and by the definition of the strategy for comet characterisation, the orbital strategy for lander delivery, and the definition and validation of the operations timeline. The definition of the landing site selection process involved almost all components of the mission team; Rosetta has been the first, and so far only mission, that could not rely on data collected by previous missions for the landing site selection. This forced the teams to include an intensive observation campaign as a mandatory part of the process; several science teams actively contributed to this campaign thus making results from science observations part of the mandatory operational products. The time allocated to the comet characterisation phase was in the order of a few weeks and all the processes, tools, and interfaces required an extensive planning an validation. Being the descent of Philae purely ballistic, the main driver for the orbital strategy was the capability to accurately control the position and velocity of Rosetta at Philae’s separation. The resulting operations timeline had to merge this need of frequent orbit determination and control with the complexity of the ground segment and the inherent risk of problems when doing critical activities in short times. This paper describes the contribution of the Mission Control Centre (MOC) at the European Space Operations Centre (ESOC) to this mission phase and the lessons learned that can be derived from this experience. [ABSTRACT FROM AUTHOR]

The international Rosetta mission was launched on 2nd March 2004 and after its ten year journey, arrived at its target destination of comet 67P/Churyumov-Gerasimenko, during 2014. Following the January 2014 exit from a two and half year hibernation period, Rosetta approached and arrived at the comet in August 2014. In November 2014, the Philae lander was deployed from Rosetta onto the comet׳s surface after which the orbiter continued its approximately one and a half year comet escort phase. The Rosetta Science Ground Segment׳s primary roles within the project are to support the Project Scientist and the Science Working Team, in order to ensure the coordination, development, validation and delivery of the desired science operations plans and their associated operational products throughout the mission., whilst also providing support to the Principle Investigator teams (including the Philae lander team) in order to ensure the provision of adequate data to the Planetary Science Archive. The lead up to, and execution of, the November 2014 Philae landing, and the subsequent Philae activities through 2015, have presented numerous unique challenges to the project teams. This paper discusses these challenges, and more specifically, their impact on the overall mission science planning activities. It details how the Rosetta Science Ground Segment has addressed these issues in collaboration with the other project teams in order to accommodate Philae operations within the continually evolving Rosetta science planning process. [ABSTRACT FROM AUTHOR]

Rosetta is an ambitious mission launched in March 2004 to study comet 67P/Churyumov–Gerasimenko. It is composed of a space probe (Rosetta) and the Philae Lander. The mission is a series of premieres: among others, first probe to escort a comet, first time a landing site is selected with short turnaround time, first time a lander has landed on a comet nucleus. In November 2014, once stabilized on the comet, Philae has performed its “First Science Sequence”. Philae’s aim was to perform detailed and innovative in-situ experiments on the comet’s surface to characterize the nucleus by performing mechanical, chemical and physical investigations on the comet surface. The main contribution to the Rosetta lander by the French space agency (CNES) is the Science Operation and Navigation Center (SONC) located in Toulouse. Among its tasks is the scheduling of the scientific activities of the 10 lander experiments and then to provide it to the Lander Control Center (LCC) located in DLR Cologne. The teams in charge of the Philae activity scheduling had to cope with considerable constraints in term of energy, data management, asynchronous processes and co-activities or exclusions between instruments. Moreover the comet itself, its environment and the landing conditions remained unknown until separation time. The landing site was selected once the operational sequence was already designed. This paper will explain the specific context of the Rosetta lander mission and all the constraints that the lander activity scheduling had to face to fulfill the scientific objectives specified for Philae. A specific tool was developed by CNES and used to design the complete sequence of activities on the comet with respect to all constraints. The baseline scenario for the lander operation will also be detailed as well as the sequence performed on the comet to highlight the difficulties and challenges that the operational team faced. [ABSTRACT FROM AUTHOR]

Structure-based protein design tests our understanding of the minimal determinants of protein structure and function. Previous studies have demonstrated that placing zinc binding amino acids (His, Glu, Asp or Cys) near each other in a folded protein in an arrangement predicted to be tetrahedral is often sufficient to achieve binding to zinc. However, few designs have been characterized with high-resolution structures. Here, we use X-ray crystallography, binding studies and mutation analysis to evaluate three alternative strategies for designing zinc binding sites with the molecular modeling program Rosetta. While several of the designs were observed to bind zinc, crystal structures of two designs reveal binding configurations that differ from the design model. In both cases, the modeling did not accurately capture the presence or absence of second-shell hydrogen bonds critical in determining binding-site structure. Efforts to more explicitly design second-shell hydrogen bonds were largely unsuccessful as evidenced by mutation analysis and low expression of proteins engineered with extensive primary and secondary networks. Our results suggest that improved methods for designing interaction networks will be needed for creating metal binding sites with high accuracy. [ABSTRACT FROM AUTHOR]

Forcefields used in biomolecular simulations are comprised of energetic terms that are physical in nature, based on parameter fitting to quantum mechanical simulation or experimental data, or statistical, drawing off high-resolution structural data to describe distributions of molecular features. Combining the two in a single forcefield is challenging, since physical terms describe some, but not all, of the observed statistics, leading to double counting. In this manuscript, we develop a general scheme for correcting statistical potentials used in combination with physical terms. We apply these corrections to the sidechain torsional potential used in the Rosetta all-atom forcefield. We show the approach identifies instances of double-counted interactions, including electrostatic interactions between sidechain and nearby backbone, and steric interactions between neighboring Cβ atoms within secondary structural elements. Moreover, this scheme allows for the inclusion of intraresidue physical terms, previously turned off to avoid overlap with the statistical potential. Combined, these corrections lead to a forcefield with improved performance on several structure prediction tasks, including rotamer prediction and native structure discrimination. [ABSTRACT FROM AUTHOR]

Background: The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts. Results: We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among all proteins, including the newly discovered PA-X protein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. M1, M2, PB1-F2, PB1 and PB2 of H1N1 subtype, in addition to H1N1 signatures, also carry H3N2 signatures. Similarly M1, M2, NP, NS1, NEP and PB2 of H3N2 subtype were shown to carry both H3N2 and H1N1 host-specific signatures (HSSs). Conclusions: To sum it up, we computationally constructed simple IF-THEN rule-based models that could distinguish between aa sequences of avian and human IAVs. From the rules we identified HSSs having a potential to affect the adaptation to specific hosts. The identification of combinatorial HSSs suggests that the process of adaptation of IAVs to a new host is more complex than previously suggested. The present study provides a basis for further detailed studies with the aim to elucidate the molecular mechanisms providing the foundation for the adaptation process. [ABSTRACT FROM AUTHOR]

Consideration is given to the estimates for the strength of the consolidated material forming the bulk of the nucleus of comet 67P Churyumov-Gerasimenko and those for the strength of the surface material overlying the consolidated material at the sites of the first and last contact of the Philae lander with the nucleus. The strength of the consolidated material was estimated by analyzing the terrain characteristics of the steep cliffs, where the material is exposed on the surface. Based on these estimates, the tensile strength of the material is in the range from 1.5 to 100 Pa; the shear strength, from ∼13 to ⩾30 Pa; and the compressive strength, from 30 to 150 Pa, possibly up to 1.5 kPa. These are very low strength values. Given the dependence of the measurement results on the size of the measured object, they are similar to those of fresh dry snow at -10°C. The (compressive) strength of the surface material at the site of the first touchdown of Philae on the nucleus is estimated from the measurements of the dynamics of the surface impact by the spacecraft's legs and the geometry of the impact pits as 1-3 kPa. For comparison with the measurement results for ice-containing materials in terrestrial laboratories, it needs to be taken into account that the rate of deformation by Philae's legs is four orders of magnitude higher than that in typical terrestrial measurements, leading to a possible overestimation of the strength by roughly an order of magnitude. There was an attemp to put one of the MUPUS sensors into the surface material at the site of the last contact of Philae with the nucleus. Noticeable penetration of the tester probe was not achieved that led to estimation of the minimum compressive strength of the material to be ⩾4 MPa4 This fairly high strength appears to indicate the presence of highly porous ice with grains 'frozen' at contacts. [ABSTRACT FROM AUTHOR]

Incorporating the world's largest ever pumping station, the Toshka Project sets out to make a vast area of Egypt's Western Desert suitable for agriculture, industry and habitation, both assisting national food security and relieving pressure on cities to accommodate a growing population. Architect and urban designer Charlotte Malterre-Barthes evaluates the project and sets it in the context of a long line of ambitious territorial transformation and irrigation schemes centred around the Nile. [ABSTRACT FROM AUTHOR]

We protein engineers are ambivalent about evolution: on the one hand, evolution inspires us with myriad examples of biomolecular binders, sensors, and catalysts; on the other hand, these examples are seldom well-adapted to the engineering tasks we have in mind. Protein engineers have therefore modified natural proteins by point substitutions and fragment exchanges in an effort to generate new functions. A counterpoint to such design efforts, which is being pursued now with greater success, is to completely eschew the starting materials provided by nature and to design new protein functions from scratch by using de novo molecular modeling and design. While important progress has been made in both directions, some areas of protein design are still beyond reach. To this end, we advocate a synthesis of these two strategies: by using design calculations to both recombine and optimize fragments from natural proteins, we can build stable and as of yet un-sampled structures, thereby granting access to an expanded repertoire of conformations and desired functions. We propose that future methods that combine phylogenetic analysis, structure and sequence bioinformatics, and atomistic modeling may well succeed where any one of these approaches has failed on its own. [ABSTRACT FROM AUTHOR]

The landing of the ROSETTA-mission lander Philae on November 12th 2014 on Comet 67 P/Churyumov-Gerasimenko was planned as a descent with passive landing and anchoring by harpoons at touch-down. Actually the lander was not fixed at touch-down to the ground due to failing harpoons. The lander internal damper was actuated at touch-down for 42.6 mm with a speed of 0.08 m/s while the lander touch-down speed was 1 m/s. The kinetic energy before touch-down was 50 J, 45 J were dissipated by the lander internal damper and by ground penetration at touch-down, and 5 J kinetic energy are left after touch-down (0.325 m/s speed). Most kinetic energy was dissipated by ground penetration (41 J) while only 4 J are dissipated by the lander internal damper. Based on these data, a value for a constant compressive soil-strength of between 1.55 kPa and 1.8 kPa is calculated. This paper focuses on the reconstruction of the touch-down at Agilkia over a period of around 20 s from first ground contact to lift-off again. After rebound Philae left a strange pattern on ground documented by the OSIRIS Narrow Angle Camera (NAC). The analysis shows, that the touch-down was not just a simple damped reflection on the surface. Instead the lander had repeated contacts with the surface over a period of about 20 s±10 s. This paper discusses scenarios for the reconstruction of the landing sequence based on the data available and on computer simulations. Simulations are performed with a dedicated mechanical multi-body model of the lander, which was validated previously in numerous ground tests. The SIMPACK simulation software was used, including the option to set forces at the feet to the ground. The outgoing velocity vector is mostly influenced by the timing of the ground contact of the different feet. It turns out that ground friction during damping has strong impact on the lander outgoing velocity, on its rotation, and on its nutation. After the end of damping, the attitude of the lander can be strongly changed by the additional ground contacts even with the flywheel still running inside the lander. The simulation shows that the outbound velocity vector and the lander rotation were formed immediately at touch-down during the first 1.5 s. The outbound velocity vector is found to be formed by the ground slope and the lander damping characteristic, especially the nearly horizontal flight out. [ABSTRACT FROM AUTHOR]

Recent measurements of the volatile composition of the coma of Comet 67P/Churyumov–Gerasimenko (hereafter 67P) allow constraints to be set on the origin of volatile elements (water, carbon, nitrogen, noble gases) in inner planets' atmospheres. Analyses by the ROSINA mass spectrometry system onboard the Rosetta spacecraft indicate that 67P ice has a D/H ratio three times that of the ocean value ( Altwegg et al., 2015 ) and contains significant amounts of N 2 , CO, CO 2 , and importantly, argon ( Balsiger et al., 2015 ). Here we establish a model of cometary composition based on literature data and the ROSINA measurements. From mass balance calculations, and provided that 67P is representative of the cometary ice reservoir, we conclude that the contribution of cometary volatiles to the Earth's inventory was minor for water (≤1%), carbon (≤1%), and nitrogen species (a few % at most). However, cometary contributions to the terrestrial atmosphere may have been significant for the noble gases. They could have taken place towards the end of the main building stages of the Earth, after the Moon-forming impact and during either a late veneer episode or, more probably, the Terrestrial Late Heavy Bombardment around 4.0–3.8 billion years (Ga) ago. Contributions from the outer solar system via cometary bodies could account for the dichotomy of the noble gas isotope compositions, in particular xenon, between the mantle and the atmosphere. A mass balance based on 36 Ar and organics suggests that the amount of prebiotic material delivered by comets could have been quite considerable – equivalent to the present-day mass of the biosphere. On Mars, several of the isotopic signatures of surface volatiles (notably the high D/H ratios) are clearly indicative of atmospheric escape processes. Nevertheless, we suggest that cometary contributions after the major atmospheric escape events, e.g., during a Martian Late Heavy Bombardment towards the end of the Noachian era, could account for the Martian elemental C/N/ 36 Ar ratios, solar-like krypton isotope composition and high 15 N/ 14 N ratios. Taken together, these observations are consistent with the volatiles of Earth and Mars being trapped initially from the nebular gas and local accreting material, then progressively added to by contributions from wet bodies from increasing heliocentric distances. Overall, no unified scenario can account for all of the characteristics of the inner planet atmospheres. Advances in this domain will require precise analysis of the elemental and isotopic compositions of comets and therefore await a cometary sample return mission. [ABSTRACT FROM AUTHOR]

Energy functions, fragment libraries, and search methods constitute three key components of fragment-assembly methods for protein structure prediction, which are all crucial for their ability to generate high-accuracy predictions. All of these components are tightly coupled; efficient searching becomes more important as the quality of fragment libraries decreases. Given these relationships, there is currently a poor understanding of the strengths and weaknesses of the sampling approaches currently used in fragment-assembly techniques. Here, we determine how the performance of search techniques can be assessed in a meaningful manner, given the above problems. We describe a set of techniques that aim to reduce the impact of the energy function, and assess exploration in view of the search space defined by a given fragment library. We illustrate our approach using Rosetta and EdaFold, and show how certain features of these methods encourage or limit conformational exploration. We demonstrate that individual trajectories of Rosetta are susceptible to local minima in the energy landscape, and that this can be linked to non-uniform sampling across the protein chain. We show that EdaFold's novel approach can help balance broad exploration with locating good low-energy conformations. This occurs through two mechanisms which cannot be readily differentiated using standard performance measures: exclusion of false minima, followed by an increasingly focused search in low-energy regions of conformational space. Measures such as ours can be helpful in characterizing new fragment-based methods in terms of the quality of conformational exploration realized. [ABSTRACT FROM AUTHOR]

The year 2014 was an historic and challenging time for the Rosetta mission. On 20 January the spacecraft awoke from a 957-day hibernation; by August, it had arrived at Comet 67P/Churyumov-Gerasimenko; and in November, the lander Philae was deployed to the comet's surface. These milestones were communicated by traditional outreach channels--on websites and via press events--as well as through the extensive use of social media. To provide an opportunity for the public to participate actively in these milestones, the European Space Agency and its partners ran three competitions. In this article we outline how these competitions provided a means for the public to engage with what was to become one of the most exciting space science missions in decades. [ABSTRACT FROM AUTHOR]

The Rosetta mission is a milestone in terms of science and public outreach. The European Space Agency and the Deutsches Zentrum für Luft- und Raumfahrt in particular did a marvellous job of sparking global public interest, driven by various events throughout the mission. In contrast, the actions of the Max Planck Society research group in charge of the high resolution Optical, Spectroscopic, and Infrared Remote Imaging System 1 were, in my opinion, the cause of some concern and bring to light an important debate in the relationship between outreach and science. This article seeks to review the outreach that surrounded the Rosetta mission and to highlight both the best practice that made it a success and the bad practice that set some aspects behind.2 [ABSTRACT FROM AUTHOR]

Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modeling, which combines computational tools recently developed in our laboratory: the database of protein domain structures (BDDB) with one dimensional and three dimensional threading applications. The protocol was tested during a CASP11 experiment.