Protein Structure Refinement and Prediction via NMR Chemical Shifts and Quantum Chemistry

Le, Hong Biao; Pearson, John G.; Dios, Angel C. de; Oldfield, Eric

doi:10.1021/ja00118a016

Cited by 87 publications

(103 citation statements)

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“…One can either use chemical-shift tensors to provide torsional restraints in a simulated annealing program such as X-PLOR [102,114], or one can use probabilistic methods to actually predict dihedral angles based on measured chemicalshift tensors [103,105]. In either case, the complex dependence of chemical-shift tensors on their local environment must first be understood for such techniques to be possible.…”

Section: Resultsmentioning

confidence: 99%

“…In either case, the complex dependence of chemical-shift tensors on their local environment must first be understood for such techniques to be possible. [lOO,103,114,115]. The main advantage to using theoretical chemical-shift surfaces for structure prediction and refinement is that they can cover the complete Ramachandran ljJ/lfI space, whereas empirical surfaces are confined to conformations that exist in the subset of proteins that are used to create the surface.…”

Section: Resultsmentioning

confidence: 99%

“…Since the chemical shift can mathematically be The other way to obtain local structure using chemical-shift tensor surfaces is to use probabilistic methods to predict ¢ and lfI from measured CSAs. One such method is the Z-surface approach [103], which uses Bayesian probability surfaces to define the probability of any given (/J/lfl pair describing the correct local geometry. A IZ-surface is created using the formula in eq.…”

Section: Predictions Of Dihedral Angles In Solid-state Peptidesmentioning

confidence: 99%

“…The Z-surface approach was first used to predict local conformations of proteins in solution based on C a , CI3, and H a chemical shifts [103]. In solution, all three chemical fig.…”

Section: Predictions Of Dihedral Angles In Solid-state Peptidesmentioning

confidence: 99%

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Novel nuclear magnetic resonance techniques for studying biological molecules

Laws

2000

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Predictions Of Dihedral Angles In Solid-state Peptidesmentioning

confidence: 99%

“…The Z-surface approach was first used to predict local conformations of proteins in solution based on C a , CI3, and H a chemical shifts [103]. In solution, all three chemical fig.…”

Section: Predictions Of Dihedral Angles In Solid-state Peptidesmentioning

confidence: 99%

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Novel nuclear magnetic resonance techniques for studying biological molecules

Laws

2000

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“…Ab initio calculations (de Dios et al, 1993;de Dios & Oldfield, 1994Le et al, 1995;de Dios, 1996) already outlined the sensitive dependence of "C, chemical shift upon both cp, $ torsion angle variations. In addition, several previous studies of helical peptides showed that, in general, A6"C, chemical shift indexes were less affected than A6H, by periodic variations along the sequence.…”

Section: Investigation Of Conformer Populations In Partially Folded Pmentioning

confidence: 99%

A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: ¹H‐, ¹³C‐NMR, and mutational analysis

et al. 1998

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The conformational properties of an 18 residues peptide spanning the entire sequence, LIKTPAsQFDADloELRAAlsMKG, of the first helix (A-helix) of domain 2 of annexin I, were thoroughly investigated. This fragment exhibits several singular features, and in particular, two successive potential capping boxes, T3xxQ6 and DxxxEl I. The former corresponds to the native hydrogen bond network stabilizing the a helix N-terminus in the protein; the latter is a non-native capping box able to break the helix at residue Dx. and is observed in the domain 2 partially folded state. Using 2D-NMR techniques, we showed that two main populations of conformers coexist in aqueous solution. The first corresponds to a single helix extending from T3 to KI7. The second corresponds to a broken helix at residue D8. Four mutants, T3A, F7A, D8A, and El IA, were designed to further analyze the role of key amino acids in the equilibrium between the two ensembles of conformers. The sensitivity of NMR parameters to account for the variations in the populations of conformers was evaluated for each peptide. Our data show the 6"CC,, chemical shift to be the most relevant parameter. We used it to estimate the population ratio in the various peptides between the two main ensembles of conformers, the full helix and the broken helix. For the WT, El IA, and F7A peptides, these ratios are respectively 35/65, 60/40, 60/40. Our results were compared to the data obtained from helix/coil transition algorithms.Keywords: a-helix; annexins; capping box; non-native conformations; NMR; peptide; protein foldingThe conformational properties of the partially folded states of proteins are related to major aspects of their folding and stability. Ahhreviutions: CD, circular dichroism: DQF COSY, double quantum filtered correlated spectroscopy; DSS, 2,2-dimethyl-2-sylapentane-5-sulfonic acid: EDTA, ethylenediamidetetraacetic acid; NMR, nuclear magnetic resonance; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser enhancement spectroscopY; TFE, trifluoroethanol; TOCSY, total correlated spectroscopy: WT peptide, wild-type peptide; AS"C,, "C, conformational ~ndex; ASH,,, CaH conformational index; A3JNHa, jJNHo conformational index.states at the residue level, several approaches were devoted to characterizing the nature of the reference "random coil" state (Ser-

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NMR study of silk I structure ofBombyx mori silk fibroin with15N- and13C-NMR chemical shift contour plots

Asakura¹,

Demura²,

Date³

et al. 1997

Biopolymers

116

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The metastable state silk I structures of Bombyx mori silk fibroin in the solid state were studied on the basis of 15N‐ and 13C‐nmr chemical shifts of Ala, Ser, and Gly residues. The 15N cross‐polarization magic angle spinning (CP/MAS) nmr spectra of the precipitated fraction after chymotrypsin hydrolysis of B. mori silk fibroin with the silk I and silk II forms were measured to determine the 15N chemical shifts of Gly, Ala, and Ser residues. For comparison, 15N CP/MAS nmr chemical shifts of Ala were measured for [15N] Ala Philosamia cynthia ricini silk fibroin with antiparallel β‐sheet and α‐helix forms. The 13C CP/MAS nmr chemical shifts of Ala, Ser, and Gly residues of B. mori silk fibroin with the silk I and silk II forms, as well as 13C CP/MAS nmr chemical shifts of Ala residue of P. c. ricini silk fibroin with β‐sheet and α‐helix forms, are used for the examination of the silk I structure. Both silk I and α‐helix peaks are shifted to a lower field than silk II (β‐sheet) for the Cα carbons of the Ala residues, while both Cβ carbon peaks are shifted to higher field. However, the silk I peak of the 15N nucleus of the Ala residue is shifted to lower field than the silk II peak, but the α‐helix peak is shifted to high field. Thus, the difference in the structure between the silk I and α‐helix is reflected in a different manner between the 13C and 15N chemical shifts. The Cα and Cβ chemical shift contour plots for Ala and Ser residues, and the Cα plot for the Gly residue, were prepared from the Protein Data Bank data obtained for 12 proteins and used for discussing the silk I structure quantitatively from the conformation‐dependent chemical shifts. The plots reported by Le and Oldfield for 15N chemical shifts were also used for the purpose. All these chemical shift data support Fossey's model (Ala: ϕ = −80°, φ = 150°, Gly: ϕ = −150°, φ = 80°) and do not support Lotz and Keith's model (Ala: ϕ = −104.6°, φ = 112.2°, Gly: ϕ = 79.8°, φ = 49.7° or Ala: ϕ = −124.5°, φ = 88.2°, Gly: ϕ = −49.8°, φ = −76.1°) as the silk I structure. © 1997 John Wiley & Sons, Inc.

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Protein Structure Refinement and Prediction via NMR Chemical Shifts and Quantum Chemistry

Cited by 87 publications

References 0 publications

Novel nuclear magnetic resonance techniques for studying biological molecules

Novel nuclear magnetic resonance techniques for studying biological molecules

A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: ¹H‐, ¹³C‐NMR, and mutational analysis

NMR study of silk I structure ofBombyx mori silk fibroin with15N- and13C-NMR chemical shift contour plots

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Protein Structure Refinement and Prediction via NMR Chemical Shifts and Quantum Chemistry

Cited by 87 publications

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Novel nuclear magnetic resonance techniques for studying biological molecules

Novel nuclear magnetic resonance techniques for studying biological molecules

A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: 1H‐, 13C‐NMR, and mutational analysis

NMR study of silk I structure ofBombyx mori silk fibroin with15N- and13C-NMR chemical shift contour plots

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A conformational equilibrium in a protein fragment caused by two consecutive capping boxes: ¹H‐, ¹³C‐NMR, and mutational analysis