Role of protein structure and the role of individual fingers in zinc finger protein–DNA recognition: a molecular dynamics simulation study and free energy calculations

Molecular dynamics and MM_GBSA energy calculations on various zinc finger proteins containing three and four fingers bound to their target DNA gave insights into the role of each finger in the DNA binding process as part of the protein structure. The wild type Zif 268 (PDB code: 1AAY) gave a ΔG value of ??76.1 (14) kcal/mol. Zinc fingers ZF1, ZF2 and ZF3 were mutated in one experiment and in another experiment one finger was cut and the rest of the protein was studied for binding. The ΔΔG values for the Zinc Finger protein with both ZF1 and ZF2 mutated was +?80 kcal/mol, while mutating only ZF1 the ΔΔG value was +?52 kcal/mol (relative to the wild type). Cutting ZF3 and studying the protein consisting only of ZF1 linked to ZF2 gave a ΔΔG value of +?68 kcal/mol. Upon cutting ZF1, the resulting ZF2 linked to ZF3 protein gave a ΔΔG value of +?41 kcal/mol. The above results shed light on the importance of each finger in the binding process, especially the role of ZF1 as the anchoring finger followed in importance by ZF2 and ZF3. The energy difference between the binding of the wild type protein Zif268 (1AAY) and that for individual finger binding to DNA according to the formula: ΔΔG_{linkers, otherstructuralfactors}?=?ΔG_zif268???(ΔG_F1+F2+F3) gave a value?=???44.5 kcal/mol. This stabilization can be attributed to the contribution of linkers and other structural factors in the intact protein in the DNA binding process. DNA binding energies of variant proteins of the wild type Zif268 which differ in their ZF1 amino acid sequence gave evidence of a good relationship between binding energy and recognition and specificity, this finding confirms the reported vital role of ZF1 in the ZF protein scanning and anchoring to the target DNA sequence. The role of hydrogen bonds in both specific and nonspecific amino acid-DNA contacts is discussed in relation to mutations. The binding energies of variant Zinc Finger proteins confirmed the role of ZF1 in the recognition, specificity and anchoring of the zinc finger protein to DNA.     

3,17‐Dioxoandrost‐4‐en‐4‐yl acetate

The title compound, C₂₁H₂₈O₄, has a 4‐acetoxy substituent positioned on the steroid α face. The six‐membered ring A assumes a conformation intermediate between 1α,2β‐half chair and 1α‐sofa. A long Csp³—Csp³ bond is observed in ring B and reproduced in quantum‐mechanical ab initio calculations of the isolated molecule using a molecular‐orbital Hartree–Fock method. Cohesion of the crystal can be attributed to van der Waals interactions and weak C—H...O hydrogen bonds.     

The recognition of a noncanonical RNA base pair by a zinc finger protein.

BACKGROUND: The zinc finger (ZF) is the most abundant nucleic-acid-interacting protein motif. Although the interaction of ZFs with DNA is reasonably well understood, little is known about the RNA-binding mechanism. We investigated RNA binding to ZFs using the Zif268-DNA complex as a model system. Zif268 contains three DNA-binding ZFs; each independently binds a 3 base pair (bp) subsite within a 9 bp recognition sequence. RESULTS: We constructed a library of phage-displayed ZFs by randomizing the alpha helix of the Zif268 central finger. Successful selection of an RNA binder required a noncanonical base pair in the middle of the RNA triplet. Binding of the Zif268 variant to an RNA duplex containing a G.A mismatch (rG.A) is specific for RNA and is dependent on the conformation of the mismatched middle base pair. Modeling and NMR analyses revealed that the rG.A pair adopts a head-to-head configuration that counterbalances the effect of S-puckered riboses in the backbone. We propose that the structure of the rG.A duplex is similar to the DNA in the original Zif268-DNA complex. CONCLUSIONS: It is possible to change the specificity of a ZF from DNA to RNA. The ZF motif can use similar mechanisms in binding both types of nucleic acids. Our strategy allowed us to rationalize the interactions that are possible between a ZF and its RNA substrate. This same strategy can be used to assess the binding specificity of ZFs or other protein motifs for noncanconical RNA base pairs, and should permit the design of proteins that bind specific RNA structures.     

Oleana‐12(13),15(16)‐diene‐3α,28‐diyl di­acetate

The title compound, C₃₄H₅₂O₄, consists of five six‐membered rings. Barring the two rings, with double bonds, all other rings are in chair conformations. Mean‐plane and ring‐puckering calculations indicate these two rings to be in distorted‐chair conformations, with distortion towards the boat conformation. There are no strong hydrogen bonds and the structure is stabilized by van der Waals interactions only. The structure is compared with those reported for other triterpenes.     

(4‐Aminopyridine‐κN1)(phthalocyaninato‐κ4N)zinc(II) tetrahydrofuran disolvate

The title compound, [Zn(C₃₂H₁₆N₈)(C₅H₆N₂)]·2C₄H₈O, consists of one (phthalocyaninato)zinc (ZnPc) unit, a coordinated 4‐aminopyridine (4‐ap) molecule and two tetrahydrofuran (THF) solvent molecules. The central Zn atom is (4+1)‐coordinated by four isoindole N atoms of the Pc core and by the pyridine N atom of 4‐aminopyridine. The Zn atom is displaced by 0.4464 (8) Å from the isoindole N₄ plane towards the pyridine N atom. The crystal structure is stabilized by intermolecular amine–phthalocyaninate N—H...N hydrogen bonds and π–π interactions between the aggregated Pc rings, which form molecular layers, and by weak van der Waals interactions between the layers. As well as hindering the aggregation of ZnPc molecules by occupying an axial position, the amino group will add new interactions which will favor applications of ZnPc, for example, as a sensitizer of photodynamic therapy.     

Diethyl 1‐(4‐fluoro­phenyl)‐3‐(2‐furyl)‐5‐oxopyrrolidine‐2,2‐di­carboxyl­ate and diethyl 1‐(3,4‐di­chloro­phenyl)‐3‐(2‐furyl)‐5‐oxopyrrolidine‐2,2‐di­carboxyl­ate

The title compounds, C₂₀H₂₀FNO₆ and C₂₀H₁₉Cl₂NO₆, respectively, may exhibit bioactivity. In these compounds, the pyrrolidine ring adopts a conformation intermediate between envelope and half‐chair. Only one of the two ethoxy­carbonyl side chains is nearly planar. Centrosymmetric pairs are formed, and the crystal structure is stabilized by weak C—H⋯O hydrogen bonds and van der Waals interactions.     

2,6‐Di­phenylthiapyran‐4‐one

In the title compound, 2,6‐di­phenyl­thia­cyclo­hexan‐4‐one, C₁₇H₁₆OS, mirror site symmetry is retained by the mol­ecule in the solid state in the absence of C—H?X hydrogen bonds. The crystal structure is stabilized by van der Waals interactions, the shortest S?O and C?O contacts being 3.567 (2) and 3.512 (3) Å, respectively.     

The 1:1 adduct of 5‐methylbenzene‐1,3‐diol (orcin) and 1,4‐di­aza­bicyclo­[2.2.2]­octane

In the title adduct, C₆H₁₂N₂·C₇H₈O₂, the orcin and 1,4‐di­aza­bi­cyclo­[2.2.2]­octane moieties are held together by O—H⋯N hydrogen bonds. One‐dimensional chiral hydrogen‐bonded chains are formed along the b axis. Neighbouring chains are held together principally by van der Waals interactions and are interrelated by translation, resulting in a chiral layer.     

1‐Benzoyl‐3‐[(2‐benzylsulfanyl)phenyl]thiourea

In the title compound, C₂₁H₁₈N₂OS₂, a strong intramolecular N—H...O hydrogen bond [N...O = 2.642 (3) Å] between the amide N atom and the benzoyl O atom forms an almost planar six‐membered ring in the central part of the molecule. In the crystal, molecules are packed through weak N—H...S interactions. Intra‐ and intermolecular hydrogen bonds and van der Waals interactions are the stabilizing forces for the crystal structure.     

Polymeric μ‐bromo‐μ‐pyridine‐3‐carboxyl­ato‐κ3O,O′:N‐mercury(II)

The asymmetric unit of the title polymeric complex, [HgBr(C₆H₄NO₂)]_n or HgBr(nic), contains mercury coordinated via two Br atoms [Hg—Br = 2.6528 (9) and 2.6468 (9) Å], two carboxyl­ate O atoms, which form a characteristic four‐membered chelate ring [Hg—O = 2.353 (6) and 2.478 (7) Å], and an N atom [Hg—N = 2.265 (5) Å], in the form of a very irregular (3+2)‐coordination polyhedron. The pronounced irregularity of the effective Hg (3+2)‐coordination is a result of the rigid stereochemistry of the nicotinate ligand. According to the covalent and van der Waals radii criteria, the strongest bonds are Hg—Br and Hg—N. These covalent interactions form a two‐dimensional poly­mer. The puckered planes are connected by van der Waals interactions, and there are only two intermolecular C—H⋯O hydrogen bonds [3.428 (10) and 3.170 (10) Å].     

(S)‐3‐(Ammoniomethyl)‐5‐methylhexanoate (pregabalin)

The title compound, C₈H₁₇NO₂, exists as a zwitterion, adopting a propeller conformation. Molecules self‐assemble to form a hydrogen‐bonded layer parallel to the ab crystallographic plane connected by N⁺—H...O⁻ and C—H...O⁻ hydrogen bonds. These layers are stacked along the c axis and are stabilized by van der Waals interactions.     

2‐(6‐Bromopyridin‐3‐yl)‐4,4,5,5‐tetramethyl‐1,3,2‐dioxaborolane and (6‐bromopyridin‐3‐yl)boronic acid,new bifunctional building blocks for combinatorial chemistry

The first comparative study between two new heterocyclic boron derivatives, viz. a (6‐bromo­pyridin‐3‐yl)­boronic ester, C₁₁H₁₅BBrNO₂, and (6‐bromo­pyridin‐3‐yl)­boronic acid, C₅H₅BBrNO₂, shows a small but not significant difference in their C—B bond lengths, which cannot explain the experimentally observed difference in their stabilities. The crystal packing of the boronic ester consists principally of van der Waals interactions, while the boronic acid mol­ecules interact in their crystal through hydrogen bonds.     

5‐Amino‐6‐phenyl‐1,6‐di­hydro­pyridazin‐3(2H)‐one

In the title compound, C₁₀H₉N₃O, the pyridazinone moiety is essentially planar and forms a dihedral angle of 49.5 (1)° with the phenyl substituent. The molecular packing is stabilized by van der Waals interactions and hydrogen bonds.     

Halogen‐bonded adduct of 1,2‐dibromo‐1,1,2,2‐tetrafluoroethane and 1,4‐diazabicyclo[2.2.2]octane

Halogen bonding is an intermolecular interaction capable of being used to direct extended structures. Typical halogen‐bonding systems involve a noncovalent interaction between a Lewis base, such as an amine, as an acceptor and a halogen atom of a halofluorocarbon as a donor. Vapour‐phase diffusion of 1,4‐diazabicyclo[2.2.2]octane (DABCO) with 1,2‐dibromotetrafluoroethane results in crystals of the 1:1 adduct, C₂Br₂F₄·C₆H₁₂N₂, which crystallizes as an infinite one‐dimensional polymeric structure linked by intermolecular N...Br halogen bonds [2.829 (3) Å], which are 0.57 Å shorter than the sum of the van der Waals radii.     

Synthesis,crystal structures and DNA/human serum albumin binding of ternary Cu(II) complexes containing amino acids and 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino

Two water‐soluble 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino (pzta)‐based Cu(II) complexes, namely [Cu(l ‐Val)(pzta)(H₂O)]ClO₄ ( 1 ) and [Cu(l ‐Thr)(pzta)(H₂O)]ClO₄ ( 2 ) (l ‐Val: l ‐valinate; l ‐Thr: l ‐threoninate), were synthesized and characterized using elemental analyses, molar conductance measurements, spectroscopic methods and single‐crystal X‐ray diffraction. The results indicated that the molecular structures of the complexes are five‐coordinated and show a distorted square‐pyramidal geometry, in which the central copper ions are coordinated to N,N atoms of pzta and N,O atoms of amino acids. The interactions of the complexes with DNA were investigated using electronic absorption, competitive fluorescence titration, circular dichroism and viscosity measurements. These studies confirmed that the complexes bind to DNA through a groove binding mode with certain affinities (K_b = 4.71 × 10³ and 1.98 × 10³ M^?1 for 1 and 2 , respectively). The human serum albumin (HSA) binding properties of the complexes were also evaluated using fluorescence and synchronous fluorescence spectroscopies, indicating that the complexes could quench the intrinsic fluorescence of HSA in a static quenching process. The relevant thermodynamic parameters revealed the involvement of van der Waals forces and hydrogen bonds in the formation of complex–HSA systems. Finally, molecular docking technology was also used to further verify the interactions of the complexes with DNA/HSA.     

1‐(4‐Bromo­phenyl)‐3‐(4‐methyl­phenyl)­prop‐2‐en‐1‐one

In the mol­ecule of the title compound, C₁₆H₁₃BrO, the two benzene rings are rotated in opposite directions with respect to the central C—C=C—C part of the mol­ecule. The phenone O atom deviates from the least‐squares plane of the mol­ecule by 0.300 (3) Å. In the crystal structure, mol­ecules are paired through C—H⋯π interactions. The molecular pairs along [001] are hydrogen bonded through three translation‐related co‐operative hydrogen bonds in the `bay area', forming molecular chains, which are further hydrogen bonded through C—H⋯Br weak interactions, forming (010) molecular layers. In the third direction, there are only weak van der Waals interactions. The co‐operative hydrogen bonds in the `bay area' are discussed briefly.     

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one Ru^II, through the DNA base‐pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear Ru^II compounds and DNA. We report a structural NMR study on the binuclear Ru^II intercalator Λ,Λ‐B (Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺; bidppz=11,11′‐bis(dipyrido[3,2‐a:2′,3′‐c]phenazinyl, bipy = 2,2′‐bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]₂. Threading of Λ,Λ‐B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ‐B is trapped in a well‐defined surface‐bound state consisting of an eccentric minor‐groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ‐B. Molecular dynamics simulations show that this minor‐groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru²⁺ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ‐B with natural calf thymus DNA. The present minor‐groove binding mode is proposed to represent the initial surface interactions of binuclear Ru^II compounds prior to intercalation into AT‐rich DNA.     

7‐Hydroxy‐5‐methoxy‐6,8‐dimethylflavanone: a natural flavonoid

The title flavonoid [systematic name: (2S)‐7‐hydroxy‐5‐methoxy‐6,8‐dimethyl‐2‐phenyl‐3,4‐dihydrochromen‐4(2H)‐one], C₁₈H₁₈O₄, displays statistical conformational disorder, with three conformations of the molecule involving three orientations of the phenyl ring and two orientations of the fused heterocyclic ring. The conformational disorder is correlated with the isomerization equilibrium between the flavanone and chalcone forms. The conformational behaviour has a potential impact on the biological activity of this class of compounds. Moreover, π stacking interactions at van der Waals distances are present between the aromatic rings of chroman‐4‐one groups of symmetry‐related molecules. Apart from these π–π interactions, molecules are linked by strong O—H...O hydrogen bonds between hydroxy and carbonyl groups.     

N—H…X (X = Cl and Br) hydrogen bonds in three isomorphous 3,5‐dichloropyridinium salts

Specific short contacts are important in crystal engineering. Hydrogen bonds have been particularly successful and together with halogen bonds can be useful for assembling small molecules or ions into crystals. The ionic constituents in the isomorphous 3,5‐dichloropyridinium (3,5‐diClPy) tetrahalometallates 3,5‐dichloropyridinium tetrachloridozincate(II), (C₅H₄Cl₂N)₂[ZnCl₄] or (3,5‐diClPy)₂ZnCl₄, 3,5‐dichloropyridinium tetrabromidozincate(II), (C₅H₄Cl₂N)₂[ZnBr₄] or (3,5‐diClPy)₂ZnBr₄, and 3,5‐dichloropyridinium tetrabromidocobaltate(II), (C₅H₄Cl₂N)₂[CoBr₄] or (3,5‐diClPy)₂CoBr₄, arrange according to favourable electrostatic interactions. Cations are preferably surrounded by anions and vice versa ; rare cation–cation contacts are associated with an antiparallel dipole orientation. N—H…X (X = Cl and Br) hydrogen bonds and X …X halogen bonds compete as closest contacts between neighbouring residues. The former dominate in the title compounds; the four symmetrically independent pyridinium N—H groups in each compound act as donors in charge‐assisted hydrogen bonds, with halogen ligands and the tetrahedral metallate anions as acceptors. The M —X coordinative bonds in the latter are significantly longer if the halide ligand is engaged in a classical X …H—N hydrogen bond. In all three solids, triangular halogen‐bond interactions are observed. They might contribute to the stabilization of the structures, but even the shortest interhalogen contacts are only slightly shorter than the sum of the van der Waals radii.     

Cocrystallization of adamantane‐1,3‐dicarboxylic acid and 4,4′‐bipyridine

The cocrystallization of adamantane‐1,3‐dicarboxylic acid (adc) and 4,4′‐bipyridine (4,4′‐bpy) yields a unique 1:1 cocrystal, C₁₂H₁₆O₄·C₁₀H₈N₂, in the C2/c space group, with half of each molecule in the asymmetric unit. The mid‐point of the central C—C bond of the 4,4′‐bpy molecule rests on a center of inversion, while the adc molecule straddles a twofold rotation axis that passes through two of the adamantyl C atoms. The constituents of this cocrystal are joined by hydrogen bonds, the stronger of which are O—H...N hydrogen bonds [O...N = 2.6801 (17) Å] and the weaker of which are C—H...O hydrogen bonds [C...O = 3.367 (2) Å]. Alternate adc and 4,4′‐bpy molecules engage in these hydrogen bonds to form zigzag chains. In turn, these chains are linked through π–π interactions along the c axis to generate two‐dimensional layers. These layers are neatly packed into a stable crystalline three‐dimensional form via weak C—H...O hydrogen bonds [C...O = 3.2744 (19) Å] and van der Waals attractions.