Surface Engineering of Top7 to Facilitate Structure Determination

Top7 is a de novo designed protein whose amino acid sequence has no evolutional trace. Such a property makes Top7 a suitable scaffold for studying the pure nature of protein and protein engineering applications. To use Top7 as an engineering scaffold, we initially attempted structure determination and found that crystals of our construct, which lacked the terminal hexahistidine tag, showed weak diffraction in X-ray structure determination. Thus, we decided to introduce surface residue mutations to facilitate crystal structure determination. The resulting surface mutants, Top7sm1 and Top7sm2, crystallized easily and diffracted to the resolution around 1.7 Å. Despite the improved data, we could not finalize the structures due to high R values. Although we could not identify the origin of the high R values of the surface mutants, we found that all the structures shared common packing architecture with consecutive intermolecular β-sheet formation aligned in one direction. Thus, we mutated the intermolecular interface to disrupt the intermolecular β-sheet formation, expecting to form a new crystal packing. The resulting mutant, Top7sm2-I68R, formed new crystal packing interactions as intended and diffracted to the resolution of 1.4 Å. The surface mutations contributed to crystal packing and high resolution. We finalized the structure model with the R/Rfree values of 0.20/0.24. Top7sm2-I68R can be a useful model protein due to its convenient structure determination.

Isomeric 4,2′:6′,4″- and 3,2′:6′,3″-Terpyridines with Isomeric 4′-Trifluoromethylphenyl Substituents: Effects on the Assembly of Coordination Polymers with [Cu(hfacac)2] (Hhfacac = Hexafluoropentane-2,4-dione)

The isomers 4′-(4-(trifluoromethyl)phenyl)-4,2′:6′,4″-terpyridine (1), 4′-(3-(trifluoromethyl)phenyl)-4,2′:6′,4″-terpyridine (2), 4′-(4-(trifluoromethyl)phenyl)-3,2′:6′,3″-terpyridine (3), and 4′-(3-(trifluoromethyl)phenyl)-3,2′:6′,3″-terpyridine (4) have been prepared and characterized. The single crystal structures of 1 and 2 were determined. The 1D-polymers [Cu2(hfacac)4(1)2]n.2nC6H4Cl2 (Hhfacac = 1,1,1,5,5,5-hexafluoropentane-2,4-dione), [Cu(hfacac)2(2)]n.2nC6H5Me, [Cu2(hfacac)4(3)2]n.nC6H4Cl2, [Cu2(hfacac)4(3)2]n.nC6H5Cl, and [Cu(hfacac)2(4)]n.nC6H5Cl have been formed by reactions of 1, 2, 3 and 4 with [Cu(hfacac)2].H2O under conditions of crystal growth by layering and four of these coordination polymers have been formed on a preparative scale. [Cu2(hfacac)4(1)2]n.2nC6H4Cl2 and [Cu(hfacac)2(2)]n.2nC6H5Me are zig-zag chains and the different substitution position of the CF3 group in 1 and 2 does not affect this motif. Packing of the polymer chains is governed mainly by C–F...F–C contacts, and there are no inter-polymer π-stacking interactions. The conformation of the 3,2′:6′,3″-tpy unit in [Cu2(hfacac)4(3)2]n.nC6H4Cl2 and [Cu(hfacac)2(4)]n.nC6H5Cl differs, leading to different structural motifs in the 1D-polymer backbones. In [Cu(hfacac)2(4)]n.nC6H5Cl, the peripheral 3-CF3C6H4 unit is accommodated in a pocket between two {Cu(hfacac)2} units and engages in four C–Hphenyl...F–Chfacac contacts which lock the phenylpyridine unit in a near planar conformation. In [Cu2(hfacac)4(3)2]n.nC6H4Cl2 and [Cu(hfacac)2(4)]n.nC6H5Cl, π-stacking interactions between 4′-trifluoromethylphenyl-3,2′:6′,3″-tpy domains are key packing interactions, and this contrasts with the packing of polymers incorporating 1 and 2. We use powder X-ray diffraction to demonstrate that the assemblies of the coordination polymers are reproducible, and that a switch from a 4,2′:6′,4″- to 3,2′:6′,3″-tpy metal-binding unit is accompanied by a change from dominant C–F...F–C and C–F...H–C contacts to π-stacking of arene domains between ligands 3 or 4.

Maleate salts of bedaquiline

Bedaquiline is one of two important new drugs for the treatment of drug-resistant tuberculosis (TB). It is marketed in the US as its fumarate salt, but only a few salts of bedaquiline have been structurally described so far. We present here five crystal structures of bedaquilinium maleate {systematic name: [4-(6-bromo-2-methoxyquinolin-3-yl)-3-hydroxy-3-(naphthalen-1-yl)-4-phenylbutyl]dimethylazanium 3-carboxyprop-2-enoate}, C32H32BrN2O2 +·C4H3O4 −, namely, a hemihydrate, a tetrahydrofuran (THF) solvate, a mixed acetone/hexane solvate, an ethyl acetate solvate, and a solvate-free structure obtained from the acetone/hexane solvate by in situ single-crystal-to-single-crystal desolvation. All salts exhibit a 1:1 cation-to-anion ratio, with the anion present as monoanionic hydromaleate and a singly protonated bedaquilinium cation. The maleate exhibits the strong intramolecular hydrogen bond typical for cis-dicarboxylic acid anions. The conformations of the cations and packing interactions in the maleate salts are compared to those of free base bedaquiline and other bedaquilinium salts.

1,4-Dibromo-2,5-bis(phenylalkoxy)benzene Derivatives: C–Br...π(arene) Versus C–H...Br and Br...Br Interactions in the Solid State

We have prepared and characterized 1,4-dibromo-2,5-bis(2-phenylethoxy)benzene (1) and 1,4-dibromo-2,5-bis(3-phenylpropoxy)benzene (2). Their single-crystal structures confirm that, at the molecular level, they are similar with the phenylalkoxy chains in extended conformations. However, there are significant differences in packing interactions. The packing in 1 is dominated by C–Br...π(arene) interactions, with each Br located over one C–C bond of the central arene ring of an adjacent molecule. In contrast, the packing of molecules of 2 involves a combination of C–H...Br hydrogen bonds, Br...Br interactions, and arene–arene π-stacking. The single-crystal structures of both orthorhombic and triclinic polymorphs of 1 have been determined and the packing interactions are shown to be essentially identical.

Manipulating the Conformation of 3,2′:6′,3″-Terpyridine in [Cu2(μ-OAc)4(3,2′:6′,3″-tpy)]n 1D-Polymers

We report the preparation and characterization of 4′-([1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (1), 4′-(4′-fluoro-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (2), 4′-(4′-chloro-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (3), 4′-(4′-bromo-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (4), and 4′-(4′-methyl-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (5), and their reactions with copper(II) acetate. Single-crystal structures of the [Cu2(μ-OAc)4L]n 1D-coordination polymers with L = 1–5 have been determined, and powder X-ray diffraction confirms that the single crystal structures are representative of the bulk samples. [Cu2(μ-OAc)4(1)]n and [Cu2(μ-OAc)4(2)]n are isostructural, and zigzag polymer chains are present which engage in π-stacking interactions between [1,1′-biphenyl]pyridine units. 1D-chains nest into one another to give 2D-sheets; replacing the peripheral H in 1 by an F substituent in 2 has no effect on the solid-state structure, indicating that bifurcated contacts (H...H for 1 or H...F for 2) are only secondary packing interactions. Upon going from [Cu2(μ-OAc)4(1)]n and [Cu2(μ-OAc)4(2)]n to [Cu2(μ-OAc)4(3)]n, [Cu2(μ-OAc)4(4)]n, and [Cu2(μ-OAc)4(5)]n·nMeOH, the increased steric demands of the Cl, Br, or Me substituent induces a switch in the conformation of the 3,2′:6′,3″-tpy metal-binding domain, and a concomitant change in dominant packing interactions to py–py and py–biphenyl face-to-face π-stacking. The study underlines how the 3,2′:6′,3″-tpy domain can adapt to different steric demands of substituents through its conformational flexibility.

Molecular Packing Interaction in DNA Crystals

DNA crystallography provides essential structural information to understand the biochemical and biological functions of oligonucleotides. Therefore, it is necessary to understand the factors affecting crystallization of DNA to develop a strategy for production of diffraction-quality DNA crystals. We analyzed key factors affecting intermolecular interactions in 509 DNA crystals from the Nucleic Acid Database and Protein Databank. Packing interactions in DNA crystals were classified into four categories based on the intermolecular hydrogen bonds in base or backbone, and their correlations with other factors were analyzed. From this analysis, we confirmed that hydrogen bonding between terminal end and mid-region is most common in crystal packing and in high-resolution crystal structures. Interestingly, P212121 is highly preferred in DNA crystals in general, but the P61 space group is relatively abundant in A-DNA crystals. Accordingly, P212121 contains more terminal end-mid-region interactions than other space groups, confirming the significance of this interaction. While metals play a role in the production of a good crystal in B-DNA conformation, their effect is not significant in other conformations. From these analyses, we found that packing interaction and other factors have a strong influence on the quality of DNA crystals and provide key information to predict crystal growth of candidate oligonucleotides.

Switching the Conformation of 3,2′:6′,3″-tpy Domains in 4′-(4-n-Alkyloxyphenyl)-3,2′:6′,3″-Terpyridines

The preparation and characterization of 4′-(4-n-octyloxyphenyl)-3,2′:6′,3″-terpyridine (8) and 4′-(4-n-nonyloxyphenyl)-3,2′:6′,3″-terpyridine (9) are reported. The single crystal structures of 4′-(4-n-hexyloxyphenyl)-3,2′:6′,3″-terpyridine (6), 4′-(4-n-heptyloxyphenyl)-3,2′:6′,3″-terpyridine (7), and compounds 8 and 9 have been determined. The conformation of the 3,2′:6′,3″-tpy unit is trans,trans in 6 and 7, but switches to cis,trans in 8 and 9. This is associated with significant changes in the packing interactions with a more dominant role for van der Waals interactions between adjacent n-alkyloxy chains and C–Hmethylene... π interactions in 8 and 9. The solid-state structures of 6 and 7 with the n-hexyloxy and n-heptyloxy chains feature interwoven sheets of supramolecular assemblies of molecules, with pairs of n-alkyloxy chains threaded through cavities in an adjacent sheet.

Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization

Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by Fc∊RI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and Fc∊RI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with Fc∊RI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.

Structural characterization of a hybrid terpyridine–pyrazine ligand and its one-dimensional ZnII coordination polymer: a computational approach to conventional and nonconventional intermolecular interactions

The structures of a new hybrid terpyridine–pyrazine ligand, namely 4′-[4-(pyrazin-2-yl)phenyl]-4,2′:6′,4′′-terpyridine (L2), C25H17N5, and its one-dimensional coordination polymer catena-poly[[bis(acetylacetonato-κ2 O,O′)zinc]-μ-4′-[4-(pyrazin-2-yl-κN 4)phenyl]-4,2′:6′,4′′-terpyridine-κN 1], [Zn(C5H7O2)2(C25H17N5)] n or [Zn(acac)2(L2)] n (Hacac is acetylacetone), are reported. Packing interactions in both crystal structures are analyzed using Hirshfeld surface and enrichment ratio techniques. For the simpler structure of the monomeric ligand, further studies on the interaction hierarchy using the energy framework approach were made. The result was a complete picture of the intermolecular interaction landscape, which revealed some subtle details, for example, that some weak (at first sight negligible) C—H...N interactions in the structure of free L2 play a relevant role in the crystal stabilization.