scholarly journals Conformational changes in Apolipoprotein N-acyltransferase (Lnt)

2018 ◽  
Author(s):  
Benjamin Wiseman ◽  
Martin Högbom
Keyword(s):  
Conformational Changes ◽  
Crystal Packing ◽  
Cell Envelope ◽  
Crystal Form ◽  
Covalent Attachment ◽  
Gram Negative Bacteria ◽  
Asymmetric Unit ◽  
Cellular Functions ◽  
Crystal Forms ◽  
Potential Mode

SUMMARYIn bacteria, lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three essential integral membrane enzymes. The last step of this process, unique to Gram negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of this enzyme. In one form the enzyme crystallized with two molecules in the asymmetric unit. In one of those molecules the thioester acyl-intermediate is observed. In the other molecule, the crystal packing suggests one potential mode of apolipoprotein docking to Lnt. In the second crystal form the enzyme crystallized with one molecule in the asymmetric unit in an apparent apo-state remarkably devoid of any bound molecules in the large open substrate entry portal. Taken together, these structures suggest that the movement of the essential W237 is triggered by substrate binding and could help direct and stabilize the interaction between Lnt and the incoming substrate apolipoprotein.Graphical Abstract

scholarly journals Conformational changes in Apolipoprotein N-acyltransferase (Lnt)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Benjamin Wiseman ◽  
Martin Högbom
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Cell Envelope ◽  
Covalent Modification ◽  
Covalent Attachment ◽  
Gram Negative Bacteria ◽  
Cellular Functions ◽  
Crystal Forms ◽  
Active Site Cysteine ◽  
Open Conformation

AbstractLipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three integral membrane enzymes. The last step of this process, unique to Gram-negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of Lnt from Escherichia coli. In one form we observe a highly dynamic arm that is able to restrict access to the active site as well as a covalent modification to the active site cysteine consistent with the thioester acyl-intermediate. In the second form, the enzyme crystallized in an open conformation exposing the active site to the environment. In total we observe 3 unique Lnt molecules that when taken together suggest the movement of essential loops and residues are triggered by substrate binding that could control the interaction between Lnt and the incoming substrate apolipoprotein. The results provide a dynamic context for residues shown to be central for Lnt function and provide further insights into its mechanism.

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

2014 ◽  
Vol 70 (12) ◽  
pp. 3099-3109 ◽  
Author(s):  
Dmitry Zamyatkin ◽  
Chandni Rao ◽  
Elesha Hoffarth ◽  
Gabriela Jurca ◽  
Hayeong Rho ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Covalent Bond ◽  
Crystal Form ◽  
Phosphoryl Group ◽  
Nucleoside Triphosphate ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Nucleotide ◽  
Thumb Domain

The RNA-dependent RNA polymerase (RdRP) from norovirus (NV) genogroup II has previously been crystallized as an apoenzyme (APO1) in multiple crystal forms, as well as as a pre-incorporation ternary complex (PRE1) bound to Mn2+, various nucleoside triphosphates and an RNA primer-template duplex in an orthorhombic crystal form. When crystallized under near-identical conditions with a slightly different RNA primer/template duplex, however, the enzyme–RNA complex forms tetragonal crystals (anisotropic data,dmin≃ 1.9 Å) containing a complex with the primer/template bound in a backtracked state (BACK1) similar to a post-incorporation complex (POST1) in a step of the enzymatic cycle immediately following nucleotidyl transfer. The BACK1 conformation shows that the terminal nucleotide of the primer binds in a manner similar to the nucleoside triphosphate seen in the PRE1 complex, even though the terminal two phosphoryl groups in the triphosphate moiety are absent and a covalent bond is present between the α-phosphoryl group of the terminal nucleotide and the 3′-oxygen of the penultimate nucleotide residue. The two manganese ions bound at the active site coordinate to conserved Asp residues and the bridging phosphoryl group of the terminal nucleotide. Surprisingly, the conformation of the thumb domain in BACK1 resembles the open APO1 state more than the closed conformation seen in PRE1. The BACK1 complex thus reveals a hybrid state in which the active site is closed while the thumb domain is open. Comparison of the APO1, PRE1 and BACK1 structures of NV polymerase helps to reveal a more complete and complex pathway of conformational changes within a single RdRP enzyme system. These conformational changes lend insight into the mechanism of RNA translocation following nucleotidyl transfer and suggest novel approaches for the development of antiviral inhibitors.

scholarly journals Structures ofEscherichia colitryptophanase in holo and `semi-holo' forms

2015 ◽  
Vol 71 (3) ◽  
pp. 286-290 ◽  
Author(s):  
Anna Kogan ◽  
Leah Raznov ◽  
Garik Y. Gdalevsky ◽  
Rivka Cohen-Luria ◽  
Orna Almog ◽  
...  
Keyword(s):  
Pyridoxal Phosphate ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Sulfate Ions ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Open Conformation ◽  
Crystallization Conditions ◽  
Tyrosine Phenol Lyase ◽  
Polypeptide Chains

Two crystal forms ofEscherichia colitryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space groupP43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two sulfate ions bound in the vicinity of the active site. The conformation of all holo subunits is the same in both crystal forms. The structures suggest that Trpase is flexible in the apo form. Its conformation partially closes upon binding of PLP. The closed conformation might correspond to the enzyme in its active state with both cofactor and substrate bound in a similar way as in tyrosine phenol-lyase.

A new crystal form of the NSAID dexketoprofen

2019 ◽  
Vol 75 (6) ◽  
pp. 783-792 ◽  
Author(s):  
Patrizia Rossi ◽  
Paola Paoli ◽  
Andrea Ienco ◽  
Diletta Biagi ◽  
Maurizio Valleri ◽  
...  
Keyword(s):  
Single Crystal ◽  
Crystal Packing ◽  
Solid Phase ◽  
Crystal Form ◽  
Interaction Energies ◽  
Scanning Calorimetry ◽  
Short Term Treatment ◽  
Experimental Conditions ◽  
Crystal Forms ◽  
Anti Inflammatory

Dexketoprofen [(2S)-2-(3-benzoylphenyl)propanoic acid], C16H14O3, is the S-enantiomer of ketoprofen, a nonsteroidal anti-inflammatory drug (NSAID) that has analgesic, antipyretic and anti-inflammatory properties, and finds applications for the short-term treatment of mild to moderate pain. A new crystalline phase of dexketoprofen is reported. Its solid-state structure was determined by single-crystal X-ray diffraction (SCXRD). The molecular structure of the two independent molecules found in the asymmetric unit of this new phase (DXKP-β) were compared to those of the already known crystal form of dexketoprofen (DXKP-α) and with the S-enantiomer of the racemic compound. The three different conformers of dexketoprofen found in DXKP-α and DXKP-β were then investigated by computational methods. The optimized structures are very close to the corresponding starting geometries and do not differ significantly in energy. The crystal packing of DXKP-β was studied by means of Hirshfeld surface (HS) analysis; interaction energies were also calculated. A comparison with DXKP-α shows close similarities between the two crystal forms, i.e. in both cases, molecules assemble through the catemer O—H...O synthon of the carboxylic acid stabilized by additional C—H...O contacts and, accordingly, the interaction energies, as well as the contributions to the HS area, are very similar. Finally, the thermal behaviour of the two polymorphs of dexketoprofen was assessed by means of XRD (both from single crystal and microcrystalline powder) and differential scanning calorimetry (DSC); both crystal forms are stable under the experimental conditions adopted (air, 300–350 K for DXKP-α and 300–340 K DXKP-β) and no solid–solid phase transition occurs between the two crystal forms in the investigated temperature range (from 100 K up to ca 350 K).

Unravelling the chemical basis of the bathochromic shift in the lobster carapace; new crystal structures of unbound astaxanthin, canthaxanthin and zeaxanthin

2007 ◽  
Vol 63 (2) ◽  
pp. 328-337 ◽  
Author(s):  
Giuditta Bartalucci ◽  
Jennifer Coppin ◽  
Stuart Fisher ◽  
Gillian Hall ◽  
John R. Helliwell ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Bathochromic Shift ◽  
Crystal Form ◽  
Crystal Forms ◽  
Bonding Interaction ◽  
Crystallization Conditions ◽  
Intermolecular Distances

The crystal structures of the unbound carotenoids, synthetic astaxanthin (3S,3′S:3R,3′S:3R,3′R in a 1:2:1 ratio), canthaxanthin and (3R,3′S, meso)-zeaxanthin are compared with each other and the protein bound astaxanthin molecule in the carotenoprotein, β-crustacyanin. Three new crystal forms of astaxanthin have been obtained, using different crystallization conditions, comprising a chloroform solvate, a pyridine solvate and an unsolvated form. In each structure, the astaxanthin molecules, which are similar to one another, are centrosymmetric and adopt the 6-s-cis conformation; the end rings are bent out of the plane of the polyene chain by angles of −42.6 (5), −48.9 (5) and −50.4 (3)°, respectively, and are disordered, showing the presence of both R and S configurations (in a 1:1 ratio). In the crystal packing of the chloroform and pyridine solvates, the astaxanthin molecules show pair-wise end-to-end intermolecular hydrogen bonding of the adjacent 3-hydroxyl and 4-keto oxygens, whereas in the unsolvated crystal form, the hydrogen-bonding interaction is intermolecular. In addition, there are intermolecular C—H hydrogen bonds in all three structures. The canthaxanthin structure, measured at 100 and 293 K, also adopts the 6-s-cis conformation, but with disorder of one end ring only. The rotation of the end rings out of the plane of the polyene chains (ca −50 ° for each structure) is similar to that of astaxanthin. A number of possible C—H hydrogen bonds to the keto O atoms are also observed. (3R,3′S, meso)-zeaxanthin is centrosymmetric with a C5—C6—C7—C8 torsion angle of −74.9 (3)°; the molecules show pair-wise hydrogen bonding between the hydroxyl O atoms. In addition, for all the crystal structures the polyene chains were arranged one above the other, with intermolecular distances of 3.61–3.79 Å, indicating the presence of π-stacking interactions. Overall, these six crystal structures provide an ensemble of experimentally derived results that allow several key parameters, thought to influence colour tuning of the bathochromic shift of astaxanthin in crustacyanin, to be varied. The fact that the colour of each of the six crystals remains red, rather than turning blue, is therefore especially significant.

Analysis of multiple crystal forms ofBacillus subtilisBacB suggests a role for a metal ion as a nucleant for crystallization

2010 ◽  
Vol 66 (5) ◽  
pp. 635-639 ◽  
Author(s):  
M. Rajavel ◽  
B. Gopal
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Crystal Packing ◽  
Crystal Form ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Tetragonal Crystal ◽  
Crystallization Conditions ◽  
Surface Metal ◽  
X Ray Absorption

Bacillus subtilisBacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded β-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalizedB-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

scholarly journals A new crystal form of Lys48-linked diubiquitin

2010 ◽  
Vol 66 (9) ◽  
pp. 994-998 ◽  
Author(s):  
Jean-François Trempe ◽  
Nicholas R. Brown ◽  
Martin E. M. Noble ◽  
Jane A. Endicott
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Polyubiquitin Chains ◽  
Isopeptide Bond ◽  
Closed Conformation ◽  
Crystallization Conditions

Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6 Å resolution. The structure reveals an ordered isopeptide bond in atransconfiguration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage.

scholarly journals Born out of Fire and Ice: Polymorph Studies of the Antiviral Famciclovir

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 129
Author(s):  
Liana Vella-Zarb ◽  
Ulrich Baisch
Keyword(s):  
Variable Temperature ◽  
Chemical Properties ◽  
Crystal Form ◽  
X Ray Diffraction ◽  
Crystal Forms ◽  
X Ray ◽  
Physical Chemical ◽  
Diffraction Patterns ◽  
Crystalline Forms

There is much interest and focus on solid forms of famciclovir. However, in spite of the abundance of reported differences in oral bioavailability, compressibility, and other physical–chemical properties of the various crystal forms of this drug, very little precise structural analysis is available in the literature to date. The form used in the commercial formulation is the anhydrous form I. Patents and patent applications report three different anhydrous crystalline forms on the basis of unindexed powder diffraction patterns. Single-crystal and variable-temperature X-ray diffraction experiments using the commercially available anhydrous form of famciclovir were carried out and led not only to the crystal structure determination of the anhydrous form I, but also to discovery of a new crystal form of anhydrous famciclovir from powder data.

scholarly journals Tunable Nonlinear Optical Property of MnS Nanoparticles with Different Size and Crystal Form

Nanomaterials ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Zhihao Zhang ◽  
Pengchao Li ◽  
Yuzong Gu
Keyword(s):  
Optical Property ◽  
Nonlinear Optical ◽  
Nonlinear Optical Property ◽  
Nonlinear Refraction ◽  
Synthesis Method ◽  
Crystal Form ◽  
Optical Nonlinearity ◽  
Photon Absorption ◽  
Third Order ◽  
Crystal Forms

It is significant to study the reason that semiconductor material has adjustable third-order optical nonlinearity through crystal form and dimensions are changed. αMnS nanoparticles with different crystal forms and sizes were successfully prepared by one-step hydrothermal synthesis method and their size-limited third-order nonlinear optical property was tested by Z-scan technique with 30 ps laser pulses at 532 nm wavelength. Nanoparticles of different crystal forms exhibited different NLO (nonlinear optical) responses. γMnS had stronger NLO response than αMnS because of higher fluorescence quantum yield. Two-photon absorption and the nonlinear refraction are enhanced as size of nanoparticlesreduced. The nanoparticles had maximum NLO susceptibility which was 3.09 × 10−12 esu. Susceptibility of αMnS increased about nine times than that of largest nanoparticles. However, it was reduced when size was further decreased. This trend was explained by the effects of light induced dipole moments. And defects in αMnS nanoparticles also had effect on this nonlinear process. MnS nanoparticles had potential application value in optical limiting and optical modulation.

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