Proton coupled carbon-13 magnetic resonance spectra. Simple amides

Dorman, Douglas E.; Bovey, F. A.

doi:10.1021/jo00949a022

Cited by 98 publications

(44 citation statements)

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“…However, for the formyl-methionine amide, the aldehyde proton will lead to splitting of the carbonyl resonance because 1 H decoupling is not generally applied during the 13 C evolution period. The magnitude of the observed splitting is consistent with published values for one-bond couplings in formamide groups (33,34). This amide also exhibits NOEs (Fig.…”

Section: Resultssupporting

confidence: 90%

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti- trp RNA-binding attenuation protein

Sachleben

McElroy

Gollnick

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Anti-TRAP (AT) is a small zinc-binding protein that regulates tryptophan biosynthesis in Bacillus subtilis by binding to tryptophanbound trp RNA-binding attenuation protein (TRAP), thereby preventing it from binding RNA, and allowing transcription and translation of the trpEDCFBA operon. Crystallographic and sedimentation studies have shown that AT can homooligomerize to form a dodecamer, AT 12 , composed of a tetramer of trimers, AT 3 . Structural and biochemical studies suggest that only trimeric AT is active for binding to TRAP. Our chromatographic and spectroscopic data revealed that a large fraction of recombinantly overexpressed AT retains the N-formyl group (fAT), presumably due to incomplete N-formyl-methionine processing by peptide deformylase. Hydrodynamic parameters from NMR relaxation and diffusion measurements showed that fAT is exclusively trimeric (AT 3 ), while (deformylated) AT exhibits slow exchange between both trimeric and dodecameric forms. We examined this equilibrium using NMR spectroscopy and found that oligomerization of active AT 3 to form inactive AT 12 is linked to protonation of the amino terminus. Global analysis of the pH dependence of the trimer-dodecamer equilibrium revealed a near physiological pK a for the N-terminal amine of AT and yielded a pH-dependent oligomerization equilibrium constant. Estimates of excluded volume effects due to molecular crowding suggest the oligomerization equilibrium may be physiologically important. Because deprotonation favors "active" trimeric AT and protonation favors "inactive" dodecameric AT, our findings illuminate a possible mechanism for sensing and responding to changes in cellular pH.allostery | thermodynamic linkage | n-formyl methionine I n bacilli, the trp RNA-binding attenuation protein (TRAP) is responsible for responding to intracellular levels of tryptophan and regulating transcription (1-4) and translation (5-10) of six tryptophan biosynthetic genes clustered in the trpECDFBA operon (1, 11). Transcription of the gene is controlled by an attenuation mechanism, involving competing terminator and antiterminator RNA structural elements in the 5′ leader region of the mRNA. In the absence of cellular tryptophan, the antiterminator structure is favored, allowing transcription and translation of the operon. When cellular tryptophan levels are high, the amino acid binds to TRAP, which becomes activated for binding to an RNA site that overlaps the antiterminator sequence, favoring formation of the terminator; translation of these genes is regulated by a similar mechanism (1,6,9,10,(12)(13)(14). TRAP is a small protein (∼74 amino acids) that assembles into an undecameric (11-mer) ring-shaped structure, with binding sites for tryptophan arranged between neighboring TRAP protomers (15, 16). RNA binds to TRAP by wrapping around the outside of this ring (17).In Bacillus subtilis (Bsu), the protein anti-TRAP (AT), encoded by the yczA gene, provides further regulation by inhibiting mRNA binding by tryptophan-activated TRAP (13,18). AT is a zinc-bind...

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Section: Resultssupporting

confidence: 90%

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti- trp RNA-binding attenuation protein

Sachleben

McElroy

Gollnick

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…carbonyl group; this carbon is more shielded when syn to the carbonyl oxygen (E conformation) than when anti to the oxygen ( Z conformation). Identical results have been reported (18) for 6 (C(2): 120.2ppm, C(5): 118.5ppm)andforthesp3 andsp2 carbons of 7 (C(2): 7 b , 42.8, 7 a , 46.7ppm; C(10): 7 a , 138.8; 7 b , 140ppm) and for various acyclic amides (21)(22)(23). This effect, which has been attributed to the electric field of the carbonyl(21), seems to be general in the absence of steric compression (18).…”

Section: Discussionsupporting

confidence: 87%

Structure in the solid state and conformational analysis in solution of 1,4-diacetyl-1,4-dihydro-2,3-diphenylpyrazine, a potential antiaromatic heterocyclic compound

Armand¹,

Bois²,

Philoche‐Levisalles³

et al. 1982

Can. J. Chem.

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It is shown by X-ray crystallography that the 1,4-dihydropyrazine skeleton of 1,4-diacetyl-1,4-dihydro-2,3-diphenylpyrazine 2 has a boat shape. The C(2)–C(3) and C(5)–C(6) double bonds are localized; therefore 2 does not exist as an azahomoaromatic entity with 6 electrons delocalized on the ring and two electrons localized on one nitrogen atom. In the solid state 2 is in a Z, Z conformation. The 1H and 13C nmr spectra indicate that 2 exists as an equilibrium mixture of Z,E, E,E, and Z,Z conformers in CD2Cl2 at −80 °C. An unambiguous assignment of the different sets of signals has been obtained by nOe experiments performed at −80 °C. The conformer distribution is the following: 65% (Z,E), 22% (E,E), and 13% (Z,Z). The relatively low barrier to rotation about the carbonyl nitrogen bonds of the two amide groups [Formula: see text] is in line with a rather large C—N bond length (~1.375 Å) in the crystal.

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“…This was confirmed also by nuclear Overhauser enhancement (NOE) studies (Anet & Bourn, 1965;Lewin & Frucht, 1975). The same conclusion with respect to the direction of the anisochrony is derived from ~3C NMR studies on simple amides (Piccini-Leopardi & Reisse, 1981;McFarlane, 1970;Levy & Nelson, 1972;Dorman & Bovey, 1973a) and amino acids (Dorman & Bovey, 1973b;Voelter & Oster, 1973). According to this general consensus the prevailing (60%) trans rotamer in solution was assigned based on the fact that the C(9) and C(18) atoms give high-frequency shifts in this form while the N-methyl group absorbs at lower frequencies as shown by the present ~H and ~3C NMR results.…”

Section: Introduction Several Dihydrobenzofuran As Well Assupporting

confidence: 67%

Structure of the (1/1) complex cis-3-(2,5-dihydroxyphenyl)-5-hydroxy-3-methyl-2-(N-methylpropionamido)-2,3-dihydrobenzo[b]furan–(2H6)acetone, C19H21NO5.C3D6O

Urbańczyk‐Lipkowska¹,

Krajewski²,

Gluziński³

et al. 1984

Acta Crystallogr C

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Proton coupled carbon-13 magnetic resonance spectra. Simple amides

Cited by 98 publications

References 0 publications

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti- trp RNA-binding attenuation protein

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti- trp RNA-binding attenuation protein

Structure in the solid state and conformational analysis in solution of 1,4-diacetyl-1,4-dihydro-2,3-diphenylpyrazine, a potential antiaromatic heterocyclic compound

Structure of the (1/1) complex cis-3-(2,5-dihydroxyphenyl)-5-hydroxy-3-methyl-2-(N-methylpropionamido)-2,3-dihydrobenzo[b]furan–(2H6)acetone, C19H21NO5.C3D6O

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