Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt of Pseudomonas aeruginosa

β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bacterial death. Pseudomonas aeruginosa, a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in this report that Slt turns over the peptidoglycan by both exolytic and endolytic reactions, which cause glycosidic bond scission from a terminus or in the middle of the peptidoglycan, respectively. These reactions were characterized with complex synthetic peptidoglycan fragments that ranged in size from tetrasaccharides to octasaccharides. The X-ray structure of the wild-type apo Slt revealed it to be a doughnut-shaped protein. In a series of six additional X-ray crystal structures, we provide insights with authentic substrates into how Slt is enabled for catalysis for both the endolytic and exolytic reactions. The substrate for the exolytic reaction binds Slt in a canonical arrangement and reveals how both the glycan chain and the peptide stems are recognized by the Slt. We document that the apo enzyme does not have a fully formed active site for the endolytic reaction. However, binding of the peptidoglycan at the existing subsites within the catalytic domain causes a conformational change in the protein that assembles the surface for binding of a more expansive peptidoglycan between the catalytic domain and an adjacent domain. The complexes of Slt with synthetic peptidoglycan substrates provide an unprecedented snapshot of the endolytic reaction.

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination

Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.

On the application of the expected log-likelihood gain to decision making in molecular replacement

Molecular-replacement phasing of macromolecular crystal structures is often fast, but if a molecular-replacement solution is not immediately obtained the crystallographer must judge whether to pursue molecular replacement or to attempt experimental phasing as the quickest path to structure solution. The introduction of the expected log-likelihood gain [eLLG; McCoy et al. (2017), Proc. Natl Acad. Sci. USA, 114, 3637-3641] has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is the log-likelihood gain on intensity [LLGI; Read & McCoy (2016), Acta Cryst. D72, 375-387] expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error and the measurement errors in the data. It is shown how the eLLG may be used to answer the question `can I solve my structure by molecular replacement?'. However, this is only the most obvious of the applications of the eLLG. It is also discussed how the eLLG may be used to determine the search order and minimal data requirements for obtaining a molecular-replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement and likelihood-guided model pruning.

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.

ARCIMBOLDO on coiled coils

ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15-635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i.

TOPOGRAFÍA INTRANEURAL DE LA RAMA PROFUNDA DEL NERVIO ULNAR EN EL ANTEBRAZO DISTAL: ESTUDIO CADAVÉRICO. Intraneural topography of the deep branch of the ulnar nerve in the distal forearm: cadaveric study

Objetivo: estudiar la topografía intraneural de la rama profunda del nervio ulnar (RPNU) en el antebrazo distal en vistas a su identificación mediante disección intraneural mínima durante la transferencia del nervio del pronador cuadrado (NPC) a la RPNU. Materiales y métodos: En 15 antebrazos cadavéricos se fijó el paquete vasculonervioso ulnar a los planos musculares profundos cada un centímetro tomando como referencia el hueso pisiforme. Se disecó en sentido proximal la RPNU bajo microscopio quirúrgico (Olympus OME, 4-20x) y se registró su posición intraneural en base a una división en cuadrantes. Se midió la distancia desde el origen de la rama cutánea dorsal (RCD) del nervio ulnar al pisiforme y se registró su relación intraneural con la RPNU. Resultados: La RPNU se individualizó hasta 69mm (41-94) proximal al hueso pisiforme, ubicándose en el cuadrante posteromedial del nervio ulnar en el 78% (67-87), el 93% (92-93) y el 100% de los casos entre los 0-2, 3-6 y 7-9 centímetros, respectivamente. La distancia pisiforme-RCD fue de 63mm (52-83). En 11 miembros la disección de la RPNU se extendió proximalmente al origen de la RCD, ubicándose siempre entre esta última y la rama superficial del nervio ulnar. Conclusiones: La topografía intraneural de la RPNU en el sitio óptimo para su sección en vistas a su anastomosis con el NPC es predecible en la mayoría de los casos, lo que confirma la viabilidad de su identificación precisa mediante disección intraneural mínima.  Objective: to assess the intraneural anatomy of the deep branch of the ulnar nerve (DBUN) in the distal forearm in reference to its identification by means of minimal intraneural dissection during pronator quadratus nerve to DBUN transfers. Materials and methods: In 15 cadaveric forearms the ulnar neurovascular bundle was identified and attached to the subjacent muscles every one centimeter. Pisiform bone was used as reference. Intraneural proximal dissection of the deep branch of the ulnar nerve was performed under magnification (Olympus OME, 4-20x) and its intraneural position was registered using a quadrants scheme. Distance from pisiform to the origin of the dorsal cutaneous branch of the ulnar nerve (DCB) was measured and its intraneural position relative to DBUN was identified. Results: The DBUN could be identified up to 69mm (41-94) proximal to the pisiform and occupied the posteromedial quadrant of the ulnar nerve in 78% (67-87), 93% (92-93) and 100% of the cases in the 0-2, 3-6 and 7-9cm ranges, respectively. Distance from pisiform to the origin of the DCB was 63mm (52-83). The DBUN could be identified proximal to the origin of the DCB in 11 forearms, being located between the latter and the superficial branch of the ulnar nerve in all this cases.  Conclusions: Intraneural topography of the DBUN in the most appropriate site for its identification during its anastomosis to the PQN is predictable in the majority of cases, which supports the viability of safe identification of the de DBUN by means of minimal intraneural dissection.

Combining phase information in reciprocal space for molecular replacement with partial models

ARCIMBOLDO allows ab initio phasing of macromolecular structures below atomic resolution by exploiting the location of small model fragments combined with density modification in a multisolution frame. The model fragments can be either secondary-structure elements predicted from the sequence or tertiary-structure fragments. The latter can be derived from libraries of typical local folds or from related structures, such as a low-homology model that is unsuccessful in molecular replacement. In all ARCIMBOLDO applications, fragments are searched for sequentially. Correct partial solutions obtained after each fragment-search stage but lacking the necessary phasing power can, if combined, succeed. Here, an analysis is presented of the clustering of partial solutions in reciprocal space and of its application to a set of different cases. In practice, the task of combining model fragments from an ARCIMBOLDO run requires their referral to a common origin and is complicated by the presence of correct and incorrect solutions as well as by their not being independent. The F-weighted mean phase difference has been used as a figure of merit. Clustering perfect, non-overlapping fragments dismembered from test structures in polar and nonpolar space groups shows that density modification before determining the relative origin shift enhances its discrimination. In the case of nonpolar space groups, clustering of ARCIMBOLDO solutions from secondary-structure models is feasible. The use of partially overlapping search fragments provides a more favourable circumstance and was assessed on a test case. Applying the devised strategy, a previously unknown structure was solved from clustered correct partial solutions.

ARCIMBOLDO_LITE: single-workstation implementation and use

ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.

Structure of a 13-fold superhelix (almost) determined from first principles

Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.

Macromolecular ab initio phasing enforcing secondary and tertiary structure

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

Structure solution with ARCIMBOLDO using fragments derived from distant homology models

Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α-helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub-structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO-SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.

[Transumbilical cholecystectomy using hybrid technique: a new promising approach]

OBJECTIVES

The use of magnets in transumbilical cholecystectomy improves triangulation and achieves optimal critical view. However, the attraction between magnets can cause collisions and their management complicates the procedure, and this will become more important in children. In order to simplify the technique, we have developed a hybrid model with a single magnet.

MATERIAL AND METHODS

Retrospective review of cholecystectomies performed in our department between June 2011 and July 2012. The technique combines the use of a magnet and a curved grasper. Through transumbilical incision, a 12 mm trocar and another flexible 5 mm are placed. Laparoscope with working channel uses the 12 mm trocar. The magnet is introduced to the abdominal cavity using the working channel to provide cephalad retraction of gallbladder fundus. Curved grasper is run by the assistant to mobilize the infundibulum across flexible trocar. The surgeon operates through the working channel of the laparoscope.

RESULTS

Twenty-six patients were operated on with this technique. Mean age was 14 years (4-17) and weight 50 kg (18-90). 65% were girls. The mean operative time was 62 minutes (50-70) and the critical view of safety was achieved in all cases. Instrumental collision or hands crossing were not seen. There were no intraoperative or postoperative complications. The hospital stay was 1.4 +/- 0.6 days and the median follow-up 201 days (42-429).

CONCLUSIONS

The hybrid technique, combining magnet and a curved grasper, simplifies transumbilical surgery. It seems a feasible and safe for transumbilical cholecystectomy and potentially reproducible.

[Efficacy of recombinant activated factor VII for massive bleeding after cardiac surgery: experience with 32 patients]

OBJECTIVE

To determine the efficacy of recombinant activated factor VII (rFVIIa) to treat massive bleeding refractory to conventional treatment following cardiac surgery.

PATIENTS AND METHODS

Retrospective study of 32 adults who underwent cardiac surgery and received rFVIIa to treat life-threatening postoperative bleeding after conventional means of correcting coagulopathy had failed.

RESULTS

After administration of rFVIIa (90 microg x kg(-1), coagulation parameters soon became normal and blood loss decreased, with drainage going from a mean (SD) of 463 (321) mL in the hour when rFVIIa was infused to 155 (101) mL in the next hour (P < .001). Blood loss decreased by between 22% and 90% (mean, 66%), and the reduction was over 75% in 45% of the patients. Decreases in the transfusion of packed red blood cells (from 7A.4 [4.1] units to 2.7 [ 2.9] units; P < .001), plasma (from 4.7 [2.9] units to 1.6 [2.0] units; P < .001), and platelets were also noted. Mortality was 25%, although only 1 patient died from hemorrhagic shock. One patient developed thromboembolic complications (ischemic stroke).

CONCLUSION

rFVIIa was effective in treating refractory bleeding after cardiac surgery, reducing blood loss and transfusion requirements and restoring blood parameters to normal.