Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings

Grzesiek, Stephan; Cordier, Florence; Jaravine, Victor; Barfield, Michael

doi:10.1016/j.pnmrs.2004.08.001

Cited by 174 publications

(175 citation statements)

References 236 publications

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“…The asymmetric elongated shape of the GRA-ligand complex suggests susceptibility for magnetic field alignment, and indeed the mRDCs could be derived by measuring one-bond N-H or C-H splittings at three different field strengths (see Materials and Methods) or by using a J-coupling/chemical shift relationship (Grzesiek et al 2004). Figure 4A shows the comparison between the 25 mRDCs measured for residues located in the three stems and those predicted from the crystal structure.…”

Section: +mentioning

confidence: 99%

“…The asymmetric elongated shape of the 25-kDa GRA created sufficient susceptibility for magnetic field alignment for derivation of mRDCs by measuring one-bond N-H or C-H splittings at three different field strengths or by using a J-coupling/chemical shift relationship (Grzesiek et al 2004). In the first approach, the imino 15 N-H RDCs of the aptamer are derived by measuring the splittings at 500-, 600-, and 800-MHz proton frequencies.…”

Section: Rdc Measurementsmentioning

confidence: 99%

“…The C2-H2 RDCs were derived by calculating the difference between the measured splitting and the theoretical value of 203.2 Hz for AMP. The other approach makes use of the linear correlation between the strength of the imino 15 N-H scalar couplings involved in N-H-N hydrogen bonds and their chemical shift value following the equation 1 J NH = (1.016 Hz/ppm)dH N À 100.58 Hz (Grzesiek et al 2004). Using this equation, the theoretical J couplings are calculated.…”

Section: Rdc Measurementsmentioning

confidence: 99%

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Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ottink

Rampersad²,

Tessari³

et al. 2007

RNA

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All known guanine-sensing riboswitches regulate gene expression by specifically binding to guanine (G) or related analogs with high affinity to switch off transcription. The aptamers of this class of riboswitches are characterized by three helices (P1-P3), surrounding a central core of phylogenetically conserved nucleotides and a long-range loop-loop interaction. To gain more insight into the switching mechanism, we present here a comparison between the solution-state structures of the G-free and G-bound forms of the guanine aptamer from the xpt-pbuX operon of Bacillus subtilis, as derived from NMR chemical shifts and magnetic-field-induced residual dipolar couplings. The high-resolution NMR analysis shows the G-free aptamer is highly structured with parallel P2 and P3 helices and the long-range loop-loop interaction already present, implying that the structure is largely preformed to bind the ligand. Structural changes upon guanine binding are found to be localized to the central core. In the free state, the G-quadruple interaction and two base pairs of the P1 stem flanking the central core appear to be largely disordered. The ligand thus binds via a combined predetermined-induced fit mechanism, involving a previously unstructured five-residue loop of the J2-3 junction that folds over the ligand. These limited additional interactions within a preorganized setting possibly explain how the aptamer rapidly responds to ligand binding, which is necessary to switch the structural state of the expression platform within a narrow time frame before the RNA polymerase escapes the 59-UTR.

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Section: +mentioning

confidence: 99%

Section: Rdc Measurementsmentioning

confidence: 99%

Section: Rdc Measurementsmentioning

confidence: 99%

See 1 more Smart Citation

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ottink

Rampersad²,

Tessari³

et al. 2007

RNA

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show abstract

“…This review deals exclusively with experimental results leaving aside the enormous field of theoretical calculations. [1,2] For some general previous reviews, both experimental and theoretical, see Refs [2][3][4][5][6][7][8]. This review will start with the most recent aspects of intermolecular coupling constants because they are simpler, and then will examine the intramolecular case.…”

Section: Introductionmentioning

confidence: 99%

A review with comprehensive data on experimental indirect scalar NMR spin–spin coupling constants across hydrogen bonds

Alkorta

Elguero

Денисов

2008

Magnetic Reson in Chemistry

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“…1,2 Applications of NMR spectroscopy for obtaining valuable structural information for biologically important molecules such as proteins and nucleic acids have grown to an unprecedented extent. [3][4][5][6][7] Despite the marvelous progress in experimental technique, the NMR-resolved molecular structures may suffer from natural restrictions. Typically, the 1 H-1 H proton-proton distances probed with NOE (nuclear Overhauser effect) are not sufficient for an unambiguous determination of molecular structure.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Effective Chemical Shielding Anisotropy (CSA) in Peptide Backbone, Rating the Impact of CSAs on the Cross-Correlated Relaxations in l-Alanyl-l-alanine

et al. 2009

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The dependence of the effective chemical shielding anisotropy (effective CSA, Δσ eff ) on the and ψ peptide backbone torsion angles was calculated in the L-alanyl-L-alanine (LALA) peptide using the DFT method. The effects of backbone conformation, molecular charge including the cation, zwitterion, and anion forms of the LALA peptide, and the scaling taking into account the length of the dipolar vector were calculated for the effective CSAs in order to assess their structural behaviors and to predict their magnitudes which can be probed for the -sheet and R-helix backbone conformations via measurement of the cross-correlated relaxation rates (CCR rates). Twenty different CSA-DD cross-correlation mechanisms involving the amide nitrogen and carbonyl carbon chemical shielding tensors and the C R H R (R-carbon group), NH N (amide group), C R H N , NH R , C′H R , and C′H N (R ) R1, R2) dipolar vectors were investigated. The X-C R H R (X ) N, C′; R ) R1, R2) cross-correlations, which had already been studied experimentally, exhibited overall best performance of the calculated effective CSAs in the LALA molecule; they spanned the largest range of values upon variation of the ψ and torsions and depended dominantly on only one of the two backbone torsion angles. The X-NH N (X ) N, C′) cross-correlations, which had been also probed experimentally, depended on both backbone torsions, which makes their structural assignment more difficult. The N-NH R2 and N-C′H R1 crosscorrelations were found to be promising for the determination of various backbone conformations due to the large calculated range of the scaled effective CSA values and due to their predominant dependence on the ψ and torsions, respectively. The 20 calculated dependencies of effective CSAs on the two backbone torsion angles can facilitate the structural interpretation of CCR rates.

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Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings

Cited by 174 publications

References 236 publications

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism

A review with comprehensive data on experimental indirect scalar NMR spin–spin coupling constants across hydrogen bonds

Theoretical Study of the Effective Chemical Shielding Anisotropy (CSA) in Peptide Backbone, Rating the Impact of CSAs on the Cross-Correlated Relaxations in l-Alanyl-l-alanine

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