Safe management of surgical smoke in the age of COVID-19.

BACKGROUND: The COVID-19 global pandemic has resulted in a plethora of guidance and opinion from surgical societies. A controversial area concerns the safety of surgically created smoke and the perceived potential higher risk in laparoscopic surgery. METHODS: The limited published evidence was analysed in combination with expert opinion. A review was undertaken of the novel coronavirus with regards to its hazards within surgical smoke and the procedures that could mitigate the potential risks to healthcare staff. RESULTS: Using existing knowledge of surgical smoke, a theoretical risk of virus transmission exists. Best practice should consider the operating room set-up, patient movement and operating theatre equipment when producing a COVID-19 operating protocol. The choice of energy device can affect the smoke produced, and surgeons should manage the pneumoperitoneum meticulously during laparoscopic surgery. Devices to remove surgical smoke, including extractors, filters and non-filter devices, are discussed in detail. CONCLUSION: There is not enough evidence to quantify the risks of COVID-19 transmission in surgical smoke. However, steps can be undertaken to manage the potential hazards. The advantages of minimally invasive surgery may not need to be sacrificed in the current crisis.

Conformationally restricted calpain inhibitors.

The cysteine protease calpain-I is linked to several diseases and is therefore a valuable target for inhibition. Selective inhibition of calpain-I has proved difficult as most compounds target the active site and inhibit a broad spectrum of cysteine proteases as well as other calpain isoforms. Selective inhibitors might not only be potential drugs but should act as tools to explore the physiological and pathophysiological roles of calpain-I. α-Mercaptoacrylic acid based calpain inhibitors are potent, cell permeable and selective inhibitors of calpain-I and calpain-II. These inhibitors target the calcium binding domain PEF(S) of calpain-I and -II. Here X-ray diffraction analysis of co-crystals of PEF(S) revealed that the disulfide form of an α-mercaptoacrylic acid bound within a hydrophobic groove that is also targeted by a calpastatin inhibitory region and made a greater number of favourable interactions with the protein than the reduced sulfhydryl form. Measurement of the inhibitory potency of the α-mercaptoacrylic acids and X-ray crystallography revealed that the IC50 values decreased significantly on oxidation as a consequence of the stereo-electronic properties of disulfide bonds that restrict rotation around the S-S bond. Consequently, thioether analogues inhibited calpain-I with potencies similar to those of the free sulfhydryl forms of α-mercaptoacrylic acids.

Synchrotron and neutron techniques in biological crystallography.

Synchrotron radiation (SR) techniques are continuously pushing the frontiers of wavelength range usage, smaller crystal sample size, larger protein molecular weight and complexity, as well as better diffraction resolution. The new research specialism of probing functional states directly in crystals, via time-resolved Laue and freeze trapping structural studies, has been developed, with a range of examples, based on research stretching over some 20 years. Overall, SR X-ray biological crystallography is complemented by neutron protein crystallographic studies aimed at cases where much more complete hydrogen details are needed involving synergistic developments between SR and neutron Laue methods. A big new potential exists in harnessing genome databases for targeting of new proteins for structural study. Structural examples in this tutorial review illustrate new chemistry learnt from biological macromolecules.

Structure of lobster apocrustacyanin A1 using softer X-rays.

The molecular basis of the camouflage colouration of marine crustacea is often provided by carotenoproteins. The blue colour of the lobster carapace, for example, is intricately associated with a multimacromolecular 16-mer complex of protein subunits each with a bound astaxanthin molecule. The protein subunits of crustacyanin fall into two distinct subfamilies, CRTC and CRTA. Here, the crystal structure solution of the A(1) protein of the CRTC subfamily is reported. The problematic nature of the structure solution of the CRTC proteins (both C(1) and A(1)) warranted consideration and the development of new approaches. Three putative disulfides per protein subunit were likely to exist based on molecular-homology modelling against known lipocalin protein structures. With two such subunits per crystallographic asymmetric unit, this direct approach was still difficult as it involved detecting a weak signal from these sulfurs and suggested the use of softer X-rays, combined with high data multiplicity, as reported previously [Chayen et al. (2000), Acta Cryst. D56, 1064-1066]. This paper now describes the structure solution of CRTC in the form of the A(1) dimer based on use of softer X-rays (2 A wavelength). The structure solution involved a xenon derivative with an optimized xenon L(I) edge f" signal and a native data set. The hand of the xenon SIROAS phases was determined by using the sulfur anomalous signal from a high-multiplicity native data set also recorded at 2 A wavelength. For refinement, a high-resolution data set was measured at short wavelength. All four data sets were collected at 100 K. The refined structure to 1.4 A resolution based on 60 276 reflections has an R factor of 17.7% and an R(free) of 22.9% (3137 reflections). The structure is that of a typical lipocalin, being closely related to insecticyanin, to bilin-binding protein and to retinol-binding protein. This A(1) monomer or dimer can now be used as a search motif in the structural studies of the oligomeric forms alpha- and beta-crustacyanins, which contain bound astaxanthin molecules.

Crystal structure of hyaluronidase, a major allergen of bee venom.

BACKGROUND: Hyaluronic acid (HA) is the most abundant glycosaminoglycan of vertebrate extracellular spaces and is specifically degraded by a beta-1,4 glycosidase. Bee venom hyaluronidase (Hya) shares 30% sequence identity with human hyaluronidases, which are involved in fertilization and the turnover of HA. On the basis of sequence similarity, mammalian enzymes and Hya are assigned to glycosidase family 56 for which no structure has been reported yet. RESULTS: The crystal structure of recombinant (Baculovirus) Hya was determined at 1.6 A resolution. The overall topology resembles a classical (beta/alpha)(8) TIM barrel except that the barrel is composed of only seven strands. A long substrate binding groove extends across the C-terminal end of the barrel. Cocrystallization with a substrate analog revealed the presence of a HA tetramer bound to subsites -4 to -1 and distortion of the -1 sugar. CONCLUSIONS: The structure of the complex strongly suggest an acid-base catalytic mechanism, in which Glu113 acts as the proton donor and the N-acetyl group of the substrate is the nucleophile. The location of the catalytic residues shows striking similarity to bacterial chitinase which also operates via a substrate-assisted mechanism.

Apocrustacyanin A1 from the lobster carotenoprotein alpha-crustacyanin: crystallization and initial X-ray analysis involving softer X-rays.

The A1 subunit of the carotenoprotein alpha-crustacyanin, isolated from lobster carapace, has been crystallized using the vapour-diffusion method. The crystals, grown in solutions of ammonium sulfate containing methylpentanediol (MPD), diffracted to 2. 0 A. The crystals are stable to radiation. The space group of the crystals is P2(1)2(1)2(1). The unit-cell parameters are a = 41.9, b = 80.7, c = 110.8 A. 'Standard structure determination' has been unsuccessful within this crustacyanin family. Instead, an approach based on the S atoms is being undertaken involving softer X-rays at the SRS, Daresbury.

Structural characterisation of the native fetuin-binding protein Scilla campanulata agglutinin: a novel two-domain lectin.

The three-dimensional structure of a 244-residue, multivalent, fetuin-binding lectin, SCAfet, isolated from bluebell (Scilla campanulata) bulbs, has been solved at 3.3 A resolution by molecular replacement using the coordinates of the 119-residue, mannose-binding lectin, SCAman, also from bluebell bulbs. Unlike most monocot mannose-binding lectins, such as Galanthus nivalis agglutinin from snowdrop bulbs, which fold into a single domain, SCAfet contains two domains with approximately 55% sequence identity, joined by a linker peptide. Both domains are made up of a 12-stranded beta-prism II fold, with three putative carbohydrate-binding sites, one on each subdomain. SCAfet binds to the complex saccharides of various animal glycoproteins but not to simple sugars.

Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose.

Carbohydrate recognition by monocot mannose-binding lectins was studied via the crystal structure determination of daffodil (Narcissus pseudonarcissus) lectin. The lectin was extracted from daffodil bulbs, and crystallised in the presence of alpha-1,3 mannobiose. Molecular replacement methods were used to solve the structure using the partially refined model of Hippeastrum hybrid agglutinin as a search model. The structure was refined at 2.0 A resolution to a final R -factor of 18.7 %, and Rfreeof 26.7 %. The main feature of the daffodil lectin structure is the presence of three fully occupied binding pockets per monomer, arranged around the faces of a triangular beta-prism motif. The pockets have identical topology, and can bind mono-, di- or oligosaccharides. Strand exchange forms tightly bound dimers, and higher aggregation states are achieved through hydrophobic patches on the surface, completing a tetramer with internal 222-symmetry. There are therefore 12 fully occupied binding pockets per tetrameric cluster. The tetramer persists in solution, as shown with small-angle X-ray solution scattering. Extensive sideways and out-of-plane interactions between tetramers, some mediated via the ligand, make up the bulk of the lattice contacts.A fourth binding site was also observed. This is unique and has not been observed in similar structures. The site is only partially occupied by a ligand molecule due to the much lower binding affinity. A comparison with the Galanthus nivalis agglutinin/mannopentaose complex suggests an involvement of this site in the recognition mechanism for naturally occurring glycans.

Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution.

The X-ray crystal structure of native Scilla campanulata agglutinin, a mannose-specific lectin from bluebell bulbs and a member of the Liliaceae family, has been determined by molecular replacement and refined to an R value of 0.186 at 1.7 A resolution. The lectin crystallizes in space group P21212 with unit-cell parameters a = 70. 42, b = 92.95, c = 46.64 A. The unit cell contains eight protein molecules of Mr = 13143 Da (119 amino-acid residues). The asymmetric unit comprises two chemically identical molecules, A and B, related by a non-crystallographic twofold axis perpendicular to c. This dimer further associates by crystallographic twofold symmetry to form a tetramer. The fold of the polypeptide backbone closely resembles that found in the lectins from Galanthus nivalis (snowdrop) and Hippeastrum (amaryllis) and contains a threefold symmetric beta-prism made up of three antiparallel four-stranded beta-sheets. Each of the four-stranded beta-sheets (I, II and III) possesses a potential saccharide-binding site containing conserved residues; however, site II has two mutations relative to sites I and III which may prevent ligation at this site. Our study provides the first accurate and detailed description of a native (unligated) structure from this superfamily of mannose-specific bulb lectins and will allow comparisons with a number of lectin-saccharide complexes which have already been determined or are currently under investigation.

Crystallization and preliminary structural studies of Scilla campanulata lectin complexed with alpha1-6 mannobiose.

Recent work has shown that Scilla campanulata agglutinin from bluebell bulbs has a strong affinity for alpha(1,3)- and alpha(1,6)-linked mannosyl residues and possesses moderate antiretroviral activity. This lectin has been crystallized by the hanging-drop method of vapour diffusion complexed with the disaccharide mannose-alpha1,6-D-mannose. The crystals are in the space group P21212 with unit-cell dimensions a = 70.63, b = 92.79 and c = 47.25 A, and with a dimer in the asymmetric unit. The crystals diffract X-rays to beyond 1.5 A resolution at 277 K and are stable in an X-ray beam. Data to 1.6 A resolution have been collected using a MAR image-plate system at a synchrotron source and the structure of the complex has been solved by the molecular replacement method.

Scilla campanulata agglutinin crystallized in complex with the trimannoside alpha-D-man-(1-->6)-[alpha-D-man-(1-->3)]-alpha-D-Man.

The monocot mannose-specific lectin, Scilla campanulata agglutinin (SCA), from bluebell bulbs has a strong affinity for alpha1,3- and alpha1,6-linked mannosyl residues. SCA has been co-crystallized with the trisaccharide alpha-D-mannopyranosyl-(1-->6)-alpha-D-mannopyranosyl-(1-->3)-alpha-D -mannopyranoside ¿alpha-D-Man-(1-->6)-[alpha-D-Man-(1-->3)]-alpha-D-Man¿, the core structure of biantennary N-linked oligosaccharides. Crystals of the complex were obtained by the hanging-drop vapour-diffusion technique. A complete data set to 2.5 A resolution has been collected at 100 K, using a MAR image-plate system at a synchrotron source, from crystals which belong to the space group C2 with unit-cell dimensions a = 99.38, b = 119.86, c = 77.10 A and beta = 105.56 degrees. Use of a CCD detector with cryo-cooled crystals improved the resolution to 2.3 A. A molecular replacement solution, with the 2.5 A data set, using the native SCA as a search model was obtained, with six subunits per asymmetric unit.

Quaternary structure of UEA-II, the chitobiose specific lectin from gorse.

The chitobiose specific Ulex europaeus lectin II crystallizes in space group P3221 with unit-cell dimensions a = b = 105.54, c = 176.26 A. The asymmetric unit contains a complete lectin tetramer. The crystals were shown to diffract to 4.5 A on a rotating-anode source and to 2.7 A at the Daresbury synchrotron source. Molecular replacement and subsequent rigid-body refinement using data to 4.5 A yielded a solution corresponding to a tetramer very similar to that of phytohemagglutinin-L and soybean agglutinin. The monomers in the Ulex lectin tetramer are rotated approximately 5 degrees compared with the phytohemagglutinin-L and soybean agglutinin structures.

Beamline 14: a new multipole wiggler beamline for protein crystallography on the SRS.

A new multipole wiggler device has been designed for the 2.0 GeV Synchrotron Radiation Source at Daresbury Laboratory in the UK. The nine-pole 2.0 T device will provide radiation for two beamlines dedicated to protein crystallography, one of which will be of high intensity. This article provides details of the design of the two stations and outlines methods being developed to combine dealing with the high heat load from the radiation while allowing both stations to be built as close to the centre of the fan as possible.

Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin.

Maltoporin (LamB) facilitates the diffusion of maltodextrins across the outer membrane of E. coli. The structural basis for the specificity of the channel is investigated by X-ray structure analysis of maltoporin in complex with the disaccharides sucrose, trehalose, and melibiose. The sucrose complex, determined to 2.4 A resolution, shows that the glucosyl moiety is partly inserted into the channel constriction, while the bulky fructosyl residue appears to be hindered to enter the constriction, thus interfering with its further translocation. One of the glucosyl moieties of trehalose is found in a similar position as the glucosyl moiety of sucrose, whereas melibiose appears disordered when bound to maltoporin. A comparison with the previously reported maltoporin-maltose complex sheds light on the basis for sugar discrimination, and explains the different permeation rates observed for the saccharides.

Crystallization and preliminary X-ray analysis of a novel plant lectin from Calystegia sepium.

A mannose-specific lectin from Calystegia sepium has been crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The needle-shaped crystals are orthorhombic, space group C222(1) with cell dimensions a = 55.2(1), b = 55.9 (1), c = 196.1 (1) A. Fresh crystals diffract to 1.9 A resolution on a synchrotron radiation source. The asymmetric unit contains a dimer of two identical 16 kDa subunits with a packing density of 2.36 A(3) Da(-1). Intensity data have been observed beyond 2.0 A, but reasonable statistics restricted the usable range to 2.0 A.

X-ray structure solution of amaryllis lectin by molecular replacement with only 4% of the total diffracting matter.

It is often the case that analogous proteins from different species crystallize in a different form. These structures can usually be easily solved by the molecular-replacement (MR) technique, as the protein folding is very often conserved. However, the results from MR become more uncertain as the proportion of diffracting matter decreases as a result of multimericity and/or absence of some of the atoms in the model. In this paper results are presented on the structure solution of amaryllis lectin (109 residues per monomer) containing two protein molecules in the asymmetric unit. The structure was solved by MR using the Calpha coordinates of one monomer from snowdrop lectin which has 85% amino-acid sequence identity to amaryllis lectin. This represents only 6% of the non-H atoms of the protein molecule to be used for structure determination and it is a major improvement on previous reports. Further calculations were carried out in order to establish the minimum number of atoms which could be included in the model before a clear solution to the MR problem was revealed. This study showed that the structure of amaryllis lectin could still have been solved easily with 3.85% of the model, which even in the most favourable cases, will probably constitute a minimum for molecular-replacement structure solution.

Purification, crystallization and preliminary X-ray analysis of a mannose-binding lectin from bluebell (Scilla campanulata) bulbs.

Crystals have been grown of a mannose-specific lectin from bluebell (Scilla campanulata) bulbs in a form suitable for X-ray diffraction studies. The crystals, which diffract to high resolution, grew in hanging drops by vapour diffusion, equilibrating with a solution of 70% saturated ammonium sulfate at pH 4.7-4.8 at 293 K, in the absence of any mannose saccharides. Crystals are orthorhombic, P2(1)2(1)2, with unit-cell dimensions a = 70.78, b = 93.69, c = 46.92 A. The functional lectin molecule is organized as a tetramer of four identical 14 kDa subunits, with only two subunits in the asymmetric unit. Data to 1.86 A resolution have been recorded and the structure determined by the molecular replacement method.

Structure of the IIA domain of the mannose transporter from Escherichia coli at 1.7 angstroms resolution.

The mannose transporter from Escherichia coli is a member of the phosphoenolpyruvate-dependent phosphotransferase system. The multi-subunit complex couples translocation across the bacterial inner membrane with phosphorylation of the solute. A functional fragment (IIA(Man), residues 2 to 133) of the membrane-associated IIAB(Man) subunit of the mannose transporter was expressed as a selenomethionine protein, and the unphosphorylated molecule was crystallized and its structure solved by X-ray crystallography. The protein consists of a central five-stranded beta-sheet covered by helices on either face. The order of the secondary structure elements is (beta alpha)4, alpha beta. Four beta-strands are arranged in a parallel manner with strand order 2134 and are linked by helices forming right-handed cross-over connections. The fifth strand that forms one edge of the sheet and runs antiparallel to the others is swapped between the subunits of the dimeric structure. Helices D and E form a helical hairpin. Histidine 10, which is transiently phosphorylated during catalysis, is located at the topological switch-point of the structure, close to the subunit interface. Its imidazole ring is hydrogen bonded to the buried side-chain of Asp67. It is likely that Asp67 acts as a general base and thus increases the nucleophilicity of the histidine. Modeling suggests that the covalently bound phosphoryl group would be stabilized by the macrodipole of helix C. Putative interactions between IIA(Man) and the histidine-containing phosphocarrier protein are discussed.

Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway.

BACKGROUND: Maltoporin (which is encoded by the lamB gene) facilitates the translocation of maltodextrins across the outer membrane of E. coli. In particular, it is indispensable for the transport of long maltooligosaccharides, as these do not pass through non-specific porins. An understanding of this intriguing capability requires elucidation of the structural basis. RESULTS: The crystal structures of maltoporin in complex with maltose, maltotriose and maltohexaose reveal an extended binding site within the maltoporin channel. The maltooligosaccharides are in apolar van der Waals contact with the 'greasy slide', a hydrophobic path that is composed of aromatic residues and located at the channel lining. At the constriction of the channel the sugars are tightly surrounded by protein side chains and form an extensive hydrogen-bonding network with ionizable amino-acid residues. CONCLUSION: Hydrophobic interactions with the greasy slide guide the sugar into and through the channel constriction. The glucosyl-binding subsites at the channel constriction confer stereospecificity to the channel along with the ability to scavenge substrate at low concentrations.