dataesr/scientific-paragraphs-categorization huggingface dataset:
The most probable structures generated by simulations on Sic1-KID display IFSUs and considerable degree of compaction. The computational results find support in the available experimental data. For instance, intramolecular interactions in the computational models were found to be prevalently of electrostatic nature, with minor contributions of hydrophobic interactions. 117 This result is in agreement with the observed strong effect of acids and negligible effect of organic solvents on the ESI-MS spectra of this protein. 103, 117 Furthermore, the SASA estimates based on the computational models (53-65 nm 2 ) are in good agreement with those derived by the ESI-MS data for the low-charge component of the CSD (59. 78 nm 2 ). 103, 109 hese studies strongly suggest that the low-charge components frequently detected in the ESI-MS spectra of IDPs under screening of putative new members of this conformational class.
Acknowledgments This work is supported by the  Defense Threat and Reduction Agency  under contract number  HDTRA1-10-1-0073  and in part by  University of Bordeaux, European Research Council  ( FP7/2008-2013 ) grant  208702. This work was also supported by the  Atlantis-MILMI program  which supports the cooperation between  EU  and US higher education institutions. Funding support is both provided by the  Department of Education of the United States Government  under the contract # P116J080033 ,  University of Central Florida  and the  European Commission  under the contract # 2008-1750/001-001 CPT-USTRAN, Université Bordeaux 1.
Experimental The binary system of atropoisomers (-) Bis-Tetralone / (+) Bis-Tetralone was considered. This system crystallizes as a conglomerate forming system  [6]. Powder samples at various compositions were dissolved and crystallized from acetone at room temperature in 9mL glass vials. Thermal analyses of the powder samples (mass of ca. 10mg) were conducted on DSC 204 F1 (Netzsch). The data were processed by using the Netzsch-TA Proteus ® Software v 4. 8. 4. ). The phases were analyzed by XRPD (D8 Discover, Bruker) and diffractograms were compared to reference diffractograms (CSD database, CCDC) in order to assess the crystallographic nature of the polymorphs. For the system studied, the SHG activity of the powder samples obtained for different compositions was measured using the Kurtz and Perry method with the experimental setup previously described by Galland et al.
Based on this novel methodology, we are developing a computer software called MoMA (for Molecular Motion Algorithms), which implements a collection of robotics-inspired algorithms for the simulation of molecular motions. MoMA-LigPath is an application built on the MoMA software. Starting from the model of a protein-ligand complex, MoMA-LigPath computes the ligand unbinding path from the active site to the surface of the protein. In the current version, flexibility is considered only for the ligand and the protein side-chains, and only geometric constraints are involved. Computing times for simulating ligand unbinding in such a simplified case usually range from some seconds to a few minutes. Thus, this simple version is particularly well suited for a web server. Even though they satisfy only geometric feasibility, the paths generated by MoMA-LigPath can provide interesting information to biologists and chemists.
Users and usage modes MoMA-LigPath is free and open to all users. Access as an anonymous user is possible. Nevertheless, we recommend frequent users to create an account. This will enable them to access a record of the jobs they submit to the server, and to be informed about results by email. Some privacy measures are enforced: the data and results of each user are not accessible to others. However, a completely secure communication pipe between each user and the server cannot be absolutely guaranteed. Two usage modes are available to run jobs on the web server. The 'simple' mode is the standard way of using MoMA-LigPath, and should be sufficient in most cases. The 'advanced' mode enables the user to locally modify the flexibility of the molecules, and to access some parameters of the ML-RRT algorithm.
In addition, an execution report provides information about possible errors in the input file and operations performed by the program. The information contained in this file is important to diagnose MoMA-LigPath failures. A frequent reason for failure is the presence of atom overlaps in the input '. pdb' file. In a preprocessing stage, MoMA-LigPath tries to remove such collisions by slightly perturbing the conformation of the involved side-chains. If not all collisions are removed after a given number of iterations, the program execution stops. In this case, the user may solve the problem on her/his own (e. g. by energy minimizing the model of the complex), or resubmit the job with a reduced percentage of van der Waals radii. MoMA-LigPath may also fail to solve geometrically constrained problems, which would require some flexibility of the protein backbone.
Here, we consider the so-called R 6 state, which has a 3-fold symmetric toroidal shape (see Figure  1 ). This conformational state of the insulin hexamer is stabilized by bound phenolic molecules  (20). Understanding the mechanism of phenol unbinding is important because it is possibly involved in the conversion of the hexamer into the monomeric active form of insulin  (21). Note that the study of the hexameric insulin-phenol complex and of the hexamer-monomer conversion are of interest in pharmacology for the treatment of type 1 diabetes. The structure of the R 6 insulin hexamer, determined by radiographic crystallography, is available in the Protein Data Bank  (22) , with PDB ID: 1ZNJ. The corresponding '. pdb' file was used as input for MoMA-LigPath. The R 6 insulin hexamer presents six hydrophobic pockets containing bound phenol molecules.
The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF's industrial clients have been a major driving force in the evolution of the ESRF's macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments.
, 1998; McCarthy et al. , 2009) , ID23  (Nurizzo et al. , 2006; Flot et al. , 2010)  and ID29 (de  Sanctis et al. , 2012) , and currently accounts for around 50% of ESRF beam-time sales  (Mitchell et al. , 2011). Industrial clients of the MX beamlines can purchase beam time and perform their experiments themselves either at the ESRF or via remote access from their home laboratory. Alternatively, they can take advantage of the MXpress datacollection service. Here, cryocooled samples are shipped to the ESRF, where data collection is carried out by ESRF staff. In order to optimize the service offered to all users of the ESRF's structural biology beamlines, and to simplify support issues, the ESRF has embarked upon a process of automation and standardization  (Leonard et al. , 2007; Arzt et al.
Standardization and automation Industrial access to the ESRF's MX beamlines takes two main forms: experimenters carry out their own synchrotron datacollection experiments, either at the synchrotron facility itself or from their home laboratory via remote control; synchrotron data-collection experiments are outsourced to the ESRF via the MXpress data-collection service. Both forms of access require robust and reliable technology in order to ensure that beam time is used efficiently and, particularly when data collections are subcontracted out to ESRF staff, to provide value for money. To facilitate robustness and reliability, the experimental environments of all of the ESRF MX beamlines, regardless of their X-ray beam characteristics, have been standardized (see  Leonard et al. , 2007; de Sanctis et al.
The beamline database ISPyB The need, alluded to above, of industrial clients of the ESRF's MX beamlines for robust sample tracking and experiment reporting was one of the driving forces which led to the development and deployment at the ESRF in 2001 of PXWeb, a prototype LIMS combining sample tracking and experiment reporting during synchrotron-based MX experiments  (Arzt et al. , 2005). As both academic and industrial use of the ESRF's MX beamlines has expanded, information exchange between the home laboratory and the synchrotron became critical and an upgraded LIMS, ISPyB, was produced (Fig. 3 ). A recent publication describes both the current status of ISPYB and its functionality (Delageniere et al. , 2011). Perhaps the most basic function of ISPyB is the production of bar-coded dewar labels for the shipment of transport dewars to the ESRF.
Further comments may also be uploaded, for example if the crystal is known to diffract anisotropically. On the day of the experiment, logging into the beamline-control module MxCuBE with the relevant experiment number causes all information to be displayed in the MxCuBE GUI, where it can be used to drive sample loading/unloading, the creation of the directory path and image nomenclature or the execution of a data-collection pipeline  (Beteva et al. , 2006). During data collections ISPyB provides an easily accessible tool which clients at home in their laboratory can use to monitor progress in real time. Once connected to the relevant data-collection session in ISPyB via a web browser, a top-level chronological summary provides basic information concerning the individual sample data collections that have already been carried out or that are in progress.
This basic information is updated to include a summary of data-processing statistics from the ESRF's autoprocessing system  (Monaco et al. , 2012)  as and when this becomes available. More detailed information regarding experimental and beamline parameters, sample characterization and data-collection strategies calculated using the program BEST  (Bourenkov & Popov, 2010)  as implemented in EDNA  (Incardona et al. , 2009 ; see below) and the full results of automatic data processing can be accessed by selecting a particular data collection and clicking to a lower level. Here, snapshots of the sample and diffraction patterns are displayed. It is also possible to directly download files containing the processed diffraction data. The top-level datacollection summary is available in various formats, including a Portable Document Format (PDF) report.
Data are collected to answer a specific biological question and different applications require that certain characteristics of the data are optimized. Searching for protein-bound ligands in electron-density maps does not in principle require high levels of data completeness or accuracy  (Kleywegt, 2007; Dauter, 2010). However, the chances of identifying weakly bound ligands or fragments are only improved if crystallographic data are complete, accurate and to reasonably high resolution. When establishing the MXpress data-collection service a policy decision was made that in the absence of instructions to the contrary, if a sample/diffraction pattern could be indexed and the diffraction was the same or better than the required resolution communicated in the 'diffraction plan' (see above) then the best possible resolution data set with a multiplicity of $4.
Fast-readout pixel detectors and screening by data collection The use of EDNA is particularly helpful when collecting diffraction data using the PILATUS 6M pixel detector, as limitations of current image-visualization software means that it is difficult to manually determine the diffraction limits. The fast readout ($2 ms) times and high framing rates of the current generation of pixel detectors, coupled with shutterless data-collection protocols  (Hu ¨lsen et al. , 2006) , means that the collection of complete X-ray diffraction data sets may be achieved very quickly even when using the fine-'-sliced 'oscillations' recommended for such detectors  (Mueller et al. , 2012). On ESRF beamline ID29, 1800 PILATUS 6M 0. The application environment and data flow for the ISPyB database. The user's home laboratory is on the left of the figure and the synchrotron facility is on the right.
Details of experimental session scheduling are retrieved by ISPyB from the ESRF user portal database (Scientific Management Information System; SMIS). Prior to each experimental session, information (protein name, organism, safety class, diffraction plan etc. ) concerning the samples to be studied can be provided to the ISPyB database and can be downloaded to the beamline-control module (BCM) on the day of the experiment in order to guide data collection. During an experiment ISPyB records, stores and makes available to users in real time all relevant experimental parameters for each data collection as well as the results of automatic sample evaluation using EDNA and automatic data processing. collection strategies before data collection. Perhaps a more efficient use of beamlines that are equipped with such detectors would be a return to the so-called 'American method', suggested as long ago as 1983  (Rossmann & Erickson, 1983) , of 'shoot first and ask questions later' and 'standard experiments' to collect data sets using a standard strategy that takes into account crystal lifetime in the X-ray beam, using the results of automatic data processing to choose the best data set for use in subsequent analyses.
PCR conditions were: 1 cycle at 94uC for 2 min, followed by 30 cycles of 94uC for 15 s, 60uC for 30 s and 72uC for 2 min. The murE PCR fragment was ligated into the plasmid pET100D/topo (Invitrogen Corporation, Carlsbad, CA, USA) to produce the plasmid pET100D::-murE Vs. The recombinant protein encoded by this plasmid carries a MRGSHHHHHHGMASMTGGQQMGR-DLYDDDDKDHPFT sequence containing a hexa-histidine tag derived from the pET100D plasmids at the amino terminus. To confirm the fidelity of the PCR reaction, the murE ORF was sequenced from pET100D using the T7 promoter primer, 59-TAATACGACTCACTATAGGG-39 and the T7 reverse primer, 59-TAGTTATTGCTCAGCGGTGG-39. The cloned murE ORF was 100% identical to the sequences deposited in the Integrated Microbial Genomes public database (http://img. jgi. doe.
6 mm; W. R. Grace S. A. ) using 50 mM ammonium formate, pH 4. 4, as the mobile phase at a flow rate of 0. 6 mL?min 21. Radioactivity was detected with a flow detector (model LB506-C1, Berthold) using the Quicksafe Flow 2 scintillator (Zinsser Analytic) at 0. 6 mL?min 21. Quantification was performed with the Radiostar software (Berthold). Identical assay conditions were used when the L,L and D,D isomers of A 2 pm were tested as substrates. With lysine or ornithine, L-[ 14 C]-Lys or L-[ 14 C]-Orn, respectively, was used as the labeled substrate; in that case, radioactive substrate and product were separated by thin-layer chromatography on silica gel plates LK6D (Whatman) using 1-propanol/ammonium hydroxide/water (6:3:1; v/v) as the mobile phase, and the radioactive spots were located and quantified with a radioactivity scanner (Rita Star, Raytest Isotopenmebgera ¨te GmbH).
Determination of the kinetic constants For the determination of the kinetic constants, the same assay was used with various concentrations of one substrate and fixed concentrations of the others. In all cases, the enzyme concentration was chosen so that substrate consumption was ,20%, the linearity being ensured within this interval even at the lowest substrate concentration. Data were fitted to the equation v = V max S/(K m +S) by the Levenberg-Marquardt method  [19] , where v is the initial velocity and S is the substrate concentration, and values 6 standard deviation at 95% of confidence were calculated. The MDFitt software developed by M. Desmadril (UMR 8619, CNRS, Orsay, France) was used for this purpose.
Sequence alignment and homology modeling A multiple amino acid sequence alignment between the Mur ligase enzymes of V. spinosum (ZP_02928794. 1), Mycobacterium tuberculosis (CCE37632. 1), E. coli (NP_414627. 1) Chlamydia trachomatis (NP_219774. 1) and Pectobacterium carotovorum (ZP_03831119. 1) was generated using ClustalW2 (http://www. ebi. ac. uk/Tools/ msa/clustalw2/) with the Gonnet scoring matrix. The homology model of the MurE Vs protein was generated using the SWISS-MODEL Protein Modeling Server  [20, 21, 22]  (http://swissmodel. expasy. org/) using the E. coli MurE structure as a template PDB id: 1E8C  [23] , which was identified using a PSI-BLAST search of the MurE Vs protein sequence against proteins in the Protein Data Bank using the web server: (http:// blast. ncbi. nlm. nih. gov/).
The model was examined by hand for clashes and appropriate geometry using the visualization software PyMOL (The PyMOL Molecular Graphics System, Schro ¨dinger, LLC). Purification and analysis of V. spinosum PG PG was prepared and analyzed essentially according to Mengin-Lecreulx et al. [24]. Cells from 1 L of culture were harvested at 4uC and resuspended in 4% (w/v) sodium dodecyl sulfate (SDS) (10 mL?g 21 of cell wet weight) under constant and vigorous stirring at 100uC for 30 min. The suspension was incubated overnight at 25uC followed by centrifugation for 1 h at 17,000 rpm. The pellet containing crude PG was washed 5 times with 10 mL of sterile water and stored in water for further analysis. Half of the preparation was used to obtain purified PG. Briefly, the following treatments at 37uC were performed: (i) overnight incubation with 0.
Results The genome of V. spinosum contains the full complement of genes necessary for the de novo synthesis of peptidoglycan The V. spinosum genome was searched from the Integrated Microbial Genomes (IMG) database (http://www. jgi. doe. gov/) using the annotated PG synthesis pathway from Kyoto Encyclopedia of Genes and Genomes (KEGG). The search resulted in the identification of 20 genes that are known to be involved in PG metabolism. Importantly, the search identified orthologs of all the genes necessary for the de novo synthesis of PG in V. spinosum (Table  1 ).
Identification of the MurE ortholog from V. spinosum The orthologous MurE protein from V. spinosum was initially identified using the MurE protein sequence from C. trachomatis (NP_219774) as a query. The BlastP algorithm from the Integrated Microbial Genomes (IMG) database was employed. The search resulted in the identification of a putative MurE from V. spinosum annotated by the locus tag VspiD_010100019130, which is 37% identical to the C. trachomatis MurE  [10]. Overproduction and purification of murE Ligase from V. spinosum The murE Vs gene was cloned into the pET100D/topo plasmid, allowing expression of the protein with an N-terminal short peptide extension comprising a hexa-histidine tag (see Materials and Methods). E. coli BL21 DE3-CodonPlus-RIPL cells, transformed with the resulting vector pET100D::murE Vs , were grown and subjected to IPTG induction.
Sequence alignment and homology modeling To identify conserved regions of the enzyme and motifs employed during catalysis, a multiple amino acid sequence alignment was performed between MurE enzymes from V. spinosum, M. tuberculosis, E. coli, C. trachomatis and P. carotovorum using ClustalW2 (http://www. ebi. ac. uk/Tools/msa/clustalw2/). Ten of the 16 putative active site residues thought to be involved in substrate binding were conserved among all five sequences. The key DNPR motif  [23, 25, 26]  which comprises residues 409-412 in the V. spinosum sequence, was identical across all five sequences. To examine both the sequence and consider the consequences of differences within the MurE Vs active site, we developed a MurE Vs homology model. Using the MurE Vs amino acid sequence as a template, we performed a PSI-BLAST search against proteins with known structure in the Protein Data Bank.
The top hits were the MurE enzymes from M. tuberculosis and E. coli, with an identity of 38% and 37%, respectively. We chose the E. coli MurE structure (PDB id: 1E8C) as a template since this ortholog was well characterized  [23] , and generated a homology model for MurE Vs using SWISS-MODEL (http://swissmodel. expasy. org/). The QMEAN score of the homology model was 0. 55 (range is between 0 to 1) and the QMEAN Z score is 23. 51 (Fig. S2 )  [27]. As annotated in the MurE Ec structure, the MurE Vs homology model is predicted to have three domains: A, B and C (Fig. 4a ). Domain A comprises residues 1-84 and consists of a four-stranded parallel b-sheet, compared to the five-stranded b-sheet in the template MurE Ec , and the b-sheet is flanked by two helices, as in template structure. Domain B comprises residues 85-289 and consists of a central six-stranded parallel b-sheet surrounded by six a-helices.
coli and P. aeruginosa. Primary sequence analysis showed that MurE Vs contains ten out of the sixteen amino acids that make up the active site of the enzyme including the DNPR motif. The DNPR motif is conserved among MurEs that have been experimentally authenticated. A homology model, based on the well characterized MurE Ec enzyme (PDB id: 1E8C), was developed to examine the sequence further and consider the consequences of differences within the MurE Vs active site. The MurE Vs enzyme is likely to comprise three domains, A, B and C, each of which contribute amino acid residues to the active site. Nearly all of the active site moieties (10 of 16) known to interact with the substrates and products are conserved in the MurE Vs active site. Overall, the homology model is entirely consistent with our validated function of MurE Vs and suggests that the enzyme binds the substrates in a similar way to other known MurE enzymes.
Acknowledgments The authors thank  Dr. Richard Hailstone  from the  Chester F. Carlson Center for Imaging Science at RIT  for acquisition of the scanning electron microscopy image. AOH thank  Dr. Naomi Ward  from the  University of Wyoming  for graciously providing the genomic DNA of Verrucomicrobium spinosum DSM 4136 T to facilitate this work. The authors acknowledge  Matt Walters  for help with image presentation. HS acknowledges the  Royal Society of New Zealand  and the  Japan Society for the Promotion of Science Researcher Exchange Program.
S. L. S. , Brookhaven National Laboratory, U. S. A. The wavelength was selected with a Si(111) double monochromator and the incident parallel beam was monitored with an ion chamber. A Ge(111) analyzer crystal was placed after the sample and before the detector to obtain good angular resolution, whereas the out-of-plane resolution was given by slits. A NaI(Tl) scintillation detector was used to measure the diffracted radiation. For data collection at 20 K, the sample was mounted in a He closed-cycle cryostat. The RT pattern has been previously indexed with the program ITO. 23  The lattice parameters refined for this specimen are equivalent to the ones previously found  24  within reasonable error limits. A preliminary crystallographic model was obtained with the program PSSP,  21  and it was confirmed and improved with the program TOPAS.
31 he HSE06 functional is known to solve at least partly the problem of self-interaction, and it provides band-gaps usually in much better agreement with experiments than the GGA. 32 The projector augmented wave method,  33  as implemented in the Vienna Ab initio Simulation Package (VASP), 34 has been used. Lattice parameters and the non-hydrogen atom positions were taken from the RT synchrotron XRPD results, while the positions of the hydrogen atoms were optimized. To ensure convergence, a 4 × 4 × 2 k-point mesh was used to sample the Brillouin zone together with the default cutoff for the plane-wave expansion.