Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA

NMR spectroscopy combined with molecular modeling was used to characterize a heterodimeric complex with Dst and 2-ImN bound in the minor groove of d(GCCTAACAAGG)•d(CCTTGTTAGGC) (1:1:1 2-ImN•Dst•DNA complex). The imidazole-pyrrole-pyrrole ligand 2-ImN spans 5'-GTTA-3' of the TAACA•TGTTA binding site with the imidazole nitrogen specifically recognizing the guanine amino group. The Dst ligand lies along the 5'-AACA-3' sequence and complements the 2-ImN ligand in the formation of the antiparallel side-by-side heterodimeric complex. Titrations of the same site with Dst or 2-ImN alone yield homodimeric complexes (2:1 ligand.DNA) of lower stability than the 1:1:1 2-ImN•Dst•DNA complex. Dst and 2-ImN binding to d(CGCAAACTGGC)•d(GCCAGTTTGCG) was also investigated. The 1:1:1 2-ImN•Dst•DNA complex is again the most stable complex with the AAACT•AGTTT site and is similar to the TAACA•TGTTA complex. No monomeric binding of either 2-ImN or Dst was observed to either site

NMR characterization of hairpin polyamide complexes with the minor groove of DNA

Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove of DNA. Covalently linking polyamide subunits has led to designed ligands with both increased affinity and specificity. Simple aliphatic amino acid linkers serve as internal guide residues for turn vs extended binding in a head-to-tail-linked polyamide motif. Polyamides of sequence composition ImPyPy-X-PyPyPy containing linkers of incremental length (X = 3-aminopropionic acid (β), 4-aminobutyric acid (γ), or 5-aminovaleric acid (δ)) in complex with an undecamer DNA duplex containing a 5'-(A,T)G(A,T)(3)-3' target site were structurally characterized using NMR spectroscopy. Previous quantitative DNase I footprinting studies identified gamma as the highest affinity of these "turn" linkers. NMR titrations and 2D NOESY data combined with restrained molecular modeling reveal that polyamides with β, γ, and δ linkers all may adopt a hairpin structure. Modeling supports the idea that the linkers in the βand δcomplexes adopt an energetically less favorable turn geometry than the γlinker and confirms that the three-carbon γ linker is sufficient and optimal for the hairpin conformation

Structural analysis of covalent peptide dimers, bis(pyridine-2-carboxamidonetropsin)(CH_2)_(3-6), in complex with 5'-TGACT-3' sites by two-dimensional NMR

The peptide pyridine-2-carboxamidonetropsin (2-PyN) binds specifically in the minor groove of 5'-(A,T)G(A,T)C(A,T)-3' sequences as a side-by-side antiparallel dimer. Tethering two 2-PyN ligands through the nitrogens of the central pyrrole rings with propyl, butyl, pentyl and hexyl linkers affords covalent peptide dimers, bis(pyridine-2-carboxamide-netropsin)(CH_2)_(3-6), which bind in the minor groove of DNA with increased binding affinities and improved sequence specificities. Two-dimensional NMR studies of the complexes formed upon binding of these covalent peptide dimers to an oligonucleotide containing a 5'-TGACT-3' site reveal that the dimeric peptides bind as intramolecular dimers with nearly identical geometry and peptide-DNA contacts as in the (2-PyN)_2•5'-TGACT-3' complex

Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA

NMR spectroscopy combined with molecular modeling was used to characterize a heterodimeric complex with Dst and 2-ImN bound in the minor groove of d(GCCTAACAAGG)•d(CCTTGTTAGGC) (1:1:1 2-ImN•Dst•DNA complex). The imidazole-pyrrole-pyrrole ligand 2-ImN spans 5'-GTTA-3' of the TAACA•TGTTA binding site with the imidazole nitrogen specifically recognizing the guanine amino group. The Dst ligand lies along the 5'-AACA-3' sequence and complements the 2-ImN ligand in the formation of the antiparallel side-by-side heterodimeric complex. Titrations of the same site with Dst or 2-ImN alone yield homodimeric complexes (2:1 ligand.DNA) of lower stability than the 1:1:1 2-ImN•Dst•DNA complex. Dst and 2-ImN binding to d(CGCAAACTGGC)•d(GCCAGTTTGCG) was also investigated. The 1:1:1 2-ImN•Dst•DNA complex is again the most stable complex with the AAACT•AGTTT site and is similar to the TAACA•TGTTA complex. No monomeric binding of either 2-ImN or Dst was observed to either site

NMR characterization of hairpin polyamide complexes with the minor groove of DNA

Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove of DNA. Covalently linking polyamide subunits has led to designed ligands with both increased affinity and specificity. Simple aliphatic amino acid linkers serve as internal guide residues for turn vs extended binding in a head-to-tail-linked polyamide motif. Polyamides of sequence composition ImPyPy-X-PyPyPy containing linkers of incremental length (X = 3-aminopropionic acid (β), 4-aminobutyric acid (γ), or 5-aminovaleric acid (δ)) in complex with an undecamer DNA duplex containing a 5'-(A,T)G(A,T)(3)-3' target site were structurally characterized using NMR spectroscopy. Previous quantitative DNase I footprinting studies identified gamma as the highest affinity of these "turn" linkers. NMR titrations and 2D NOESY data combined with restrained molecular modeling reveal that polyamides with β, γ, and δ linkers all may adopt a hairpin structure. Modeling supports the idea that the linkers in the βand δcomplexes adopt an energetically less favorable turn geometry than the γlinker and confirms that the three-carbon γ linker is sufficient and optimal for the hairpin conformation

NMR Characterization of the Aliphatic β/β Pairing for Recognition of A·T/T·A Base Pairs in the Minor Groove of DNA

Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove of DNA. Because the curvature of four or five contiguous Im−Py rings does not perfectly match the canonical B-helix, β-alanine (β) residues have been inserted to reset the register. Complexes of three pyrrole−imidazole polyamides of sequence composition ImPyPy-X-PyPyPy-Dp, where X = Py, β, or glycine (G), bound to a 13 base pair DNA duplex containing a 9 base pair 5‘-TGTATATCA-3‘ match site were characterized by NMR. NMR titrations and NOESY data combined with restrained molecular modeling show that each polyamide adopts an extended antiparallel dimeric conformation with the ligands fully overlapped around a central Py/Py, G/G, or β/β pair. Conformational exchange is seen near the linker for the G-linked complex, but not with the β or Py linkers. In addition to providing the first direct structural evidence for formation of the aliphatic β/β pairing in the minor groove, models support the idea that the β linker of ImPyPy-β-PyPyPy-Dp provides an optimal combination of size, flexibility, and alignment of the polyamide-paired aromatic subunits in extended, dimeric 2:1 complexes

The exchange activities of [Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases

[Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min−1 mg−1). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors