scholarly journals N.m.r. determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer

1991 ◽  
Vol 279 (1) ◽  
pp. 269-281 ◽  
Author(s):  
A N Lane ◽  
T C Jenkins ◽  
D J Brown ◽  
T Brown
Keyword(s):  
Chemical Shifts ◽  
Order Rate Constant ◽  
Low Ph ◽  
Repair Enzymes ◽  
Nearest Neighbours ◽  
Anti Conformation ◽  
Local Flexibility ◽  
Backbone Conformation ◽  
Nuclear Overhauser ◽  
Mispaired Bases

A.G base-paired mismatches that occur during replication are among the most difficult to detect by repair enzymes. Such purine.purine mispairs can exist in two conformations, one of which is stabilized by protons [Gao & Patel (1988) J. Am. Chem. Soc. 110, 5178-5182]. We have undertaken a 1H-n.m.r. and 31P-n.m.r. study of the mismatched dodecamer d(CGCAAATTGGCG)2 as a function of both temperature and pH to determine the conformational features of the A.G mismatch. At pH greater than 7 the mispaired bases are each in the anti conformation and are stacked in the B-like helix. As the pH is decreased, a second conformation becomes populated (apparent pKa approx. 5.9) with concomitant changes in the chemical shifts of protons of the mispaired bases and their nearest neighbours. Data from two-dimensional nuclear-Overhauser-enhancement spectroscopy show unequivocally that, at low pH, the dominant conformation is one in which the mismatched G residues are in the syn conformation and are hydrogen-bonded to the A residues that remain in the anti conformation. Residues not adjacent to the A.G sites are almost unaffected by the transition or the mispairing, suggesting considerable local flexibility of the unconstrained duplexes. Despite the bulging of the mispaired bases, the conformation of the A(anti).G(anti) duplex is very similar to the native dodecamer, whereas the AH+(anti).G(syn) duplex shows a greater variation in the backbone conformation at the mismatched site. According to the chemical shifts, the duplex retains twofold symmetry in solution. The equilibrium between the syn and anti conformations of G9/G21 is strongly dependent on pH, but only weakly dependent on temperature (delta H approx. 16 kJ.mol-1). The first-order rate constant for the transition is approx. 9 s-1 at 283 K and approx. 60 s-1 at 298 K, with an activation enthalpy of approx. 100 kJ.mol-1. The stabilization of the A(anti).G(syn) conformation by protons is consistent with models invoking N1 protonation of adenine. Using the derived glycosidic torsion angles we have used restrained molecular dynamics to build models of the neutral and protonated d(CGCAAATTGGCG)2 oligomers. The results confirm that the A(anti).G(anti) and AH+(anti).G(syn) conformations are favoured at high pH and low pH respectively, in accord with n.m.r. and single-crystal X-ray data.

scholarly journals Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

1993 ◽  
Vol 294 (3) ◽  
pp. 899-908 ◽  
Author(s):  
I B Coutinho ◽  
D L Turner ◽  
J LeGall ◽  
A V Xavier
Keyword(s):  
Chemical Shifts ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Cytochrome C3 ◽  
X Ray ◽  
1H Nuclear Magnetic Resonance ◽  
Proton Resonances ◽  
Nuclear Overhauser

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

Controlled oxidations of benzo[a]pyrene

1986 ◽  
Vol 64 (7) ◽  
pp. 1247-1253 ◽  
Author(s):  
E. Lee-Ruff ◽  
H. Kazarians-Moghaddam ◽  
M. Katz
Keyword(s):  
Singlet Oxygen ◽  
High Field ◽  
Chemical Shifts ◽  
Product Distribution ◽  
Major Product ◽  
Nuclear Overhauser Enhancement ◽  
Nuclear Overhauser ◽  
Singlet Oxygen Reaction ◽  
Proton Chemical Shifts ◽  
Oxygen Reaction

The four diones derived from benzo[a]pyrene oxidation have been characterized by high-field nuclear magnetic resonance techniques including 2-D COSY and selective nuclear Overhauser enhancement. All the proton chemical shifts for these four quinones have been uneqivocally assigned. The direct photoxidation of benzo[a]pyrene gives a product distribution very similar to the TPP photosensitized oxygenation, suggesting singlet oxygen is involved in the former. A major product, which was characterized as the 6-seco derivative 6 and not previously reported, was detected in the singlet oxygen reaction. The presence of this product suggests a possible mechanism for quinone formation in the singlet oxygen reaction. One-electron oxidations of benzo[a]pyrene were carried out using tris(p-bromophenyl)aminium hexachloroantimonate and quenching of the radical cation with superoxide or water. The product distribution in this case was quite different from that obtained in the direct photooxidation.

Conformational Energy Calculations on the Eosinophil Chemotactic Peptide Analog Val-Gly-Ala-Glu: Comparison of Theory and Experiment

1988 ◽  
Vol 41 (12) ◽  
pp. 1841
Author(s):  
J Bremer ◽  
GL Mendz
Keyword(s):  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Minimum Energy ◽  
Conformational Energy ◽  
Coupling Constants ◽  
Amide Proton ◽  
Energy Calculations ◽  
Peptide Analog ◽  
Conformational Energy Calculations ◽  
Nuclear Overhauser

Conformational energy calculations have been employed to obtain minimum energy conformations of the peptide Val- Gly-Ala-Glu , an analogue of eosinophil chemotactic tetrapeptides. The calculated conformations of the peptide can be described as an ensemble of structures in which the C-terminal and N-terminal regions of the molecule are in close proximity. The charge state of the peptide showed a marked effect on the calculated conformation, and the results were also sensitive to the electrostatic environment. The calculations performed on the dianionic form of the molecule showed good agreement with experimental n.m.r . Data on coupling constants, amide-proton resonance chemical shifts and temperature coefficients, nuclear Overhauser effects, side-chain rotamer populations, and binding of paramagnetic ions, obtained in dimethyl sulfoxide solutions. The calculations demonstrate some of the inherent problems facing theoretical calculations of peptide structure.

A nuclear Overhauser effect difference study of the solution conformation of (6R)-prostaglandin I1

1980 ◽  
Vol 58 (23) ◽  
pp. 2649-2659 ◽  
Author(s):  
George Kotovych ◽  
Gerdy H. M. Aarts
Keyword(s):  
Proton Magnetic Resonance ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Solution Conformation ◽  
Magnetic Resonance Studies ◽  
Overhauser Effect ◽  
Complete Assignment ◽  
Effect Difference ◽  
Nuclear Overhauser

Proton magnetic resonance studies at 400 MHz allowed the complete assignment of the spectra for (6R)-prostaglandin I1 in phosphate buffer and in CDCl3 solutions. The spectral analysis was based on the nuclear Overhauser effect difference measurements, which also provide accurate chemical shifts and coupling constants. Conformational differences in the two solvents for the ring portion of the molecule are indicated.

Carbon-13 Nuclear Magnetic Resonance Studies of Compounds of the Vitamin B6 Group and Related Pyridine Derivatives

1975 ◽  
Vol 53 (16) ◽  
pp. 2406-2412 ◽  
Author(s):  
Roy D. Lapper ◽  
Henry H. Mantsch ◽  
Ian C. P. Smith
Keyword(s):  
Vitamin B6 ◽  
Pyridoxal Phosphate ◽  
Chemical Shifts ◽  
Resonance Assignments ◽  
Low Ph ◽  
Vitamin B ◽  
Pyridine Derivatives ◽  
High Ph ◽  
Methylene Groups ◽  
Predicted Values

The I3C chemical shifts and 13C–31P spin–spin couplings (where applicable) are reported for pyridoxine, pyridoxamine, pyridoxal, pyridoxamine phosphate, and pyridoxal phosphate. Resonance assignments are made by consideration of substituent chemical shift effects, as tested on an analogous series of pyridine derivatives. Increased shielding of the C4′ and C5′ methylene groups of the vitamin B6 compounds and the methyl groups of 3,4-dimethylpyridine relative to the predicted values are attributed to steric compression. In aqueous solution pyridoxal exists as the hemiacetal form, although at high pH it is in rapid equilibrium with a significant amount of the aldehyde form. Pyridoxal phosphate exists as the aldehyde at high pH, as the hydrated aldehyde at low pH, and in a slow equilibrium between detectable amounts of both species at pH 4. The 13C–31P couplings through two bonds lie in the range 4.5 ± 0.5 Hz found for a variety of other organic phosphates. The couplings through three bonds indicate a preference for a trans arrangement of the phosphorus and ring carbon-5.

Orientation of the methoxyl group in cis- and trans-2-methoxy-4-methyl-1,3-dioxanes and related compounds as inferred by 1H and 13C nmr spectroscopy. The significance of the "exo-anomeric" effect

1982 ◽  
Vol 60 (9) ◽  
pp. 1067-1072 ◽  
Author(s):  
Vanga S. Rao
Keyword(s):  
Dynamic Equilibrium ◽  
Chemical Shifts ◽  
13C Nmr Spectroscopy ◽  
Methoxyl Group ◽  
Anomeric Effect ◽  
1H And 13C Nmr ◽  
Nuclear Overhauser ◽  
Cis And Trans ◽  
In Cis ◽  
Related Compounds

Carbon-13 chemical shifts and 13C—1H couplings are reported for some substituted 2-methoxy-1,3-dioxanes and related tetrahydropyran derivatives. These data, together with nuclear Overhauser enhancement experiments, provided evidence for a favored orientation of the methoxyl group. From an analysis of the 13C chemical shifts and the magnitude of vicinal 13C—1H coupling between —OCH3 and H-2, a possible dynamic-equilibrium orientation for the methoxyl group is proposed, and an evaluation of the significance of a "generalized exo-anomeric effect" is presented.

Cation-dependent structural features of β-casein-(1–25)

2001 ◽  
Vol 356 (1) ◽  
pp. 277-286 ◽  
Author(s):  
Keith J. CROSS ◽  
N. Laila HUQ ◽  
Wendy BICKNELL ◽  
Eric C. REYNOLDS
Keyword(s):  
Calcium Ions ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Resonance Assignments ◽  
Structural Features ◽  
Complete Sequence ◽  
Sequence Motif ◽  
Sodium Ions ◽  
Medium Range ◽  
Nuclear Overhauser

Complete sequence-specific, proton-resonance assignments have been determined for the calcium phosphate-stabilizing tryptic peptide β-casein-(1–25) containing the phosphorylated sequence motif Ser(P)17-Ser(P)-Ser(P)-Glu-Glu21. Spectra of the peptide have been recorded, in separate experiments, in the presence of excess ammonium ions, sodium ions and calcium ions, and of the dephosphorylated peptide in the presence of excess sodium ions. We observed significant changes to chemical shifts for backbone and side-chain resonances that were dependent upon the nature of the cation present. Medium-range nuclear Overhauser effect (nOe) enhancements, characteristic of small structured regions in the peptide, were observed and also found to be cation dependent. The secondary structure of the peptide was characterized by sequential and medium-range (i, i+2/3/4, which denotes an interaction between residue i and residue i+2, i+3 or i+4 in the peptide) nOe connectivities, and Hα chemical shifts. Four structured regions were identified in the calcium-bound peptide: residues Arg1 to Glu4 were involved in a loop-type structure, and residues Val8 to Glu11, Ser(P)17 to Glu20 and Glu21 to Thr24 were implicated in β-turn conformations. Comparison of the patterns of medium-range nOe connectivities in β-casein-(1–25) with those in αS1-casein-(59–79) suggest that the two peptides have distinctly different conformations in the presence of calcium ions, despite having a high degree of sequential and functional similarity.

Determination of the molecular conformation of uridine in aqueous solution by proton magnetic resonance spectroscopy. Comparison with β-pseudouridine

1970 ◽  
Vol 48 (18) ◽  
pp. 2866-2870 ◽  
Author(s):  
Barry J. Blackburn ◽  
Arthur A. Grey ◽  
Ian C. P. Smith ◽  
Frank E. Hruska
Keyword(s):  
Magnetic Resonance ◽  
Proton Magnetic Resonance ◽  
Molecular Conformation ◽  
Chemical Shifts ◽  
Proton Magnetic Resonance Spectrum ◽  
Coupling Constants ◽  
Complete Analysis ◽  
Resonance Spectroscopy ◽  
Proton Coupling ◽  
Anti Conformation

A complete analysis of the 220 MHz proton magnetic resonance spectrum of aqueous uridine is reported. From the data a model for the molecular conformation is presented and compared with that of β-pseudouridine. It is concluded that in both compounds the ribose rings are in rapid equilibrium between classical puckered structures. The temperature-independence of the ribose proton coupling constants and chemical shifts suggests that all the conformers involved in this equilibrium have very similar energies. Both compounds exhibit a preference for the gauche–gauche rotamer about the exocyclic 4′—5′ bond; this conclusion is shown to be independent of the parameters in the Karplus equation or the energy minima chosen for the rotamers. The anti conformation of the uracil base is shown to exist in both compounds. It is proposed that the special structural significance of β-pseudouridine in transfer RNA must be due to the potential hydrogen bond that may be formed by the nitrogen atom at position one in uracil.

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