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.

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.

scholarly journals Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

2019 ◽  
Author(s):  
Georg Kuenze ◽  
Richard Bonneau ◽  
Julia Koehler Leman ◽  
Jens Meiler
Keyword(s):  
Protein Structure ◽  
Computational Methods ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
High Accuracy ◽  
Ligand Docking ◽  
Nmr Structure Determination ◽  
Overhauser Effect ◽  
Nuclear Overhauser ◽  
Nmr Restraints

AbstractComputational methods to predict protein structure from nuclear magnetic resonance (NMR) restraints that only require assignment of backbone signals hold great potential to study larger proteins and complexes. Additionally, computational methods designed to work with sparse data add atomic detail that is missing in the experimental restraints, allowing application to systems that are difficult to investigate. While specific frameworks in the Rosetta macromolecular modeling suite support the use of certain NMR restraint types, use of all commonly measured restraint types together is precluded. Here, we introduce a comprehensive framework into Rosetta that reconciles CS-Rosetta, PCS-Rosetta and RosettaNMR into a single framework, that, in addition to backbone chemical shifts and nuclear Overhauser effect distance restraints, leverages NMR restraints derived from paramagnetic labeling. Specifically, RosettaNMR incorporates pseudocontact shifts, residual dipolar couplings, and paramagnetic relaxation enhancements, measured at multiple tagging sites. We further showcase the generality of RosettaNMR for various modeling challenges and benchmark it on 28 structure prediction cases, eight symmetric assemblies, two protein-protein and three protein-ligand docking examples. Paramagnetic restraints generated more accurate models for 85% of the benchmark proteins and, when combined with chemical shifts, sampled high-accuracy models (≤ 2Å) in 50% of the cases.Significance StatementComputational methods such as Rosetta can assist NMR structure determination by employing efficient conformational search algorithms alongside physically realistic energy functions to model protein structure from sparse experimental data. We have developed a framework in Rosetta that leverages paramagnetic NMR data in addition to chemical shift and nuclear Overhauser effect restraints and extends RosettaNMR calculations to the prediction of symmetric assemblies, protein-protein and protein-ligand complexes. RosettaNMR generated high-accuracy models (≤ 2Å) in 50% of cases for a benchmark set of 28 monomeric and eight symmetric proteins and predicted protein-protein and protein-ligand interfaces with up to 1Å accuracy. The method expands Rosetta’s rich toolbox for integrative data-driven modeling and promises to be broadly useful in structural biology.

scholarly journals Potentially Mistaking Enantiomers for Different Compounds Due to the Self-Induced Diastereomeric Anisochronism (SIDA) Phenomenon

Symmetry ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1106
Author(s):  
Andreas Baumann ◽  
Alicja Wzorek ◽  
Vadim A. Soloshonok ◽  
Karel D. Klika ◽  
Aubry K. Miller
Keyword(s):  
Solid State ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
The Self ◽  
Equal Concentration ◽  
Chiral Compounds ◽  
Intermolecular Noe ◽  
Association Preference ◽  
Nuclear Overhauser ◽  
And Diffusion

The NMR phenomenon of self-induced diastereomeric anisochronism (SIDA) was observed with an alcohol and an ester. The alcohol exhibited large concentration-dependent chemical shifts (δ’s), which initially led us to erroneously consider whether two enantiomers were in fact atropisomers. This highlights a potential complication for the analysis of chiral compounds due to SIDA, namely the misidentification of enantiomers. A heterochiral association preference for the alcohol in CDCl3 was determined by the intermolecular nuclear Overhauser effect (NOE) and diffusion measurements, the same preference as found in the solid state. The ester revealed more subtle effects, but concentration-dependent δ’s, observation of intermolecular NOE’s, as well as distinct signals for the two enantiomers in a scalemic sample all indicated the formation of associates. Intermolecular NOE and diffusion measurements indicated that homochiral association is slightly preferred over heterochiral association in CDCl3, thus masking association for enantiopure and racemic samples of equal concentration. As observed with the alcohol, heterochiral association was preferred for the ester in the solid state. The potential problems that SIDA can cause are highlighted and constitute a warning: Due care should be taken with respect to conditions, particularly the concentration, when measuring NMR spectra of chiral compounds. Scalemic samples of both the alcohol and the ester were found to exhibit the self-disproportionation of enantiomers (SDE) phenomenon by preparative TLC, the first report of SDE by preparative TLC.

Proton magnetic resonance spectra of catechin and bromocatechin derivatives: C6- vs. C8-substitution

1986 ◽  
Vol 64 (10) ◽  
pp. 1998-2005 ◽  
Author(s):  
E. Kiehlmann ◽  
A. S. Tracey
Keyword(s):  
Magnetic Resonance ◽  
Proton Magnetic Resonance ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Overhauser Effect ◽  
Resonance Frequencies ◽  
The Difference ◽  
Nuclear Overhauser ◽  
Unambiguous Assignment ◽  
Magnetic Resonance Spectra

The 1Hmr spectra of 20 catechin derivatives substituted at C-6/C-8 by bromine and/or hydrogen and at oxygen by methyl, acetyl, and/or hydrogen have been analyzed in deuterated acetone, acetonitrile, and chloroform. Because of its dependence on the nature of the solvent and of the oxygen substituent, the difference between H-6 and H-8 chemical shifts has been found to be an unreliable criterion for the distinction between 8-bromo and 6-bromo isomers. In methylated catechins, double irradiation of H-8 and H-6 enhances one (MeO-7) and two (MeO-5 and MeO-7) methoxy signals, respectively, via the nuclear Overhauser effect. This permits unambiguous assignment of chemical shifts to all ring A protons. The H-6 and H-8 resonance frequencies of catechin have been determined by decoupling of the OH-5 and OH-7 protons.

A nuclear Overhauser effect difference study and a two-dimensional J proton magnetic resonance study of (6S)-prostaglandin I1

1981 ◽  
Vol 59 (10) ◽  
pp. 1449-1454 ◽  
Author(s):  
George Kotovych ◽  
Gerdy H. M. Aarts ◽  
Tom T. Nakashima
Keyword(s):  
Magnetic Resonance ◽  
Proton Magnetic Resonance ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Two Dimensional ◽  
Overhauser Effect ◽  
Effect Difference ◽  
Proton Resonances ◽  
Nuclear Overhauser

High-field nuclear Overhauser effect difference measurements allowed the assignment of the proton resonances for (6S)-prostaglandin I1 in phosphate buffer solutions. The two-dimensional J proton magnetic resonance experiments complemented these studies, as they also allowed the structure of several multiplets to be obtained when these multiplets are hidden by nearby resonances in a normal spectrum. The chemical shifts and coupling constants are compared with the data obtained previously for (6R)-prostaglandin I1.

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