Inscriere cercetatori

Site nou !

Daca nu va puteti recupera parola (sau aveti alte probleme), scrieti-ne la pagina de contact. Situl vechi se gaseste la adresa old.ad-astra.ro

Facebook

Relationships between NMR parameters and protein structure: Evaluation of isotropic chemical shifts, chemical shift anisotropy tensors, and scalar coupling through covalent and hydrogen bonds

Domenii publicaţii > Biologie + Tipuri publicaţii > Tezã de doctorat (nepublicatã)

Autori: Gabriel Cornilescu

Editorial: UMI, Bell & Howell, 2000.

Rezumat:

Isotropic and anisotropic chemical shielding, together with scalar and dipolar coupling, are NMR observables that contain information of key importance for protein structural studies.
We present a database program (TALOS) that searches for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. Tests carried out for proteins of known structure indicate that the root-mean-square difference between the output of TALOS and the X-ray derived backbone angles is about 15 degrees.
The changes in solute chemical shift between an isotropic and a liquid crystalline phase provide information on the magnitude and orientation of the chemical shift anisotropy (CSA) tensor relative to the molecule’s alignment tensor (determined from the observed dipolar couplings and their known orientation in the three-dimensional structure of the molecule). Assuming all atoms of a given type have the same CSA tensor, the magnitude and orientation of the average 13C’, 15N and HN CSA tensors were determined. For HN, the scatter is completely dominated by intrinsic variations in the CSA tensor at the different sites. The degree of correlation between observed and predicted variations in 13C’ or 15N chemical shifts is dominated by the uncertainty in the protein structure and can be used as a sensitive monitor for evaluating the quality of that structure, or alternatively the difference between observed and predicted 13C’ or 15N chemical shift variations can be used as a driving force in calculating the protein’s structure.
It is demonstrated that scalar couplings between a hydrogen bond donating 15N nucleus and a hydrogen bond accepting C=O group can readily be observed in uniformly 13C/15N-enriched ubiquitin. Over the small range of N-O hydrogen bond lengths (2.8-3.3 Angstrom) for which 3hJNC’ couplings are observable, the measured 3hJNC’ values in a binding domain of Streptococcal protein G can be fit to: 3hJNC’ = -59000 exp(-4RNO) +/- 0.09 Hz, or RNO = 2.75 – 0.25 ln(-3hJNC’) +/- 0.06 Angstrom. The sign of 3hJNC’, determined from a zero-quantum/double-quantum experiment, is found to be the same as that of the 1JNH coupling, i.e. negative.
One-bond 1JCaCb scalar couplings, measured in ubiquitin, exhibit a strong dependence on the local backbone conformation. Empirically, the deviation from the 1JCaCb value measured in the corresponding free amino acid, can be expressed as delta(1JCaCb) = 1.3 + 0.6 cos(psi-61°) + 2.2 cos[2(psi-61°)] – 0.9 cos[2(phi + 20°)] +/- 0.5 Hz, where phi and psi are the intraresidue polypeptide backbone torsion angles obtained from ubiquitin’s X-ray structure. The relation between 1JCaCb and backbone torsion angles is confirmed by density functional theory (DFT) calculations on the peptide analog Ace-Ala-NMe.
Isotropic and anisotropic chemical shielding, together with scalar and dipolar coupling, are NMR observables that contain information of key importance for protein structural studies.
We present a database program (TALOS) that searches for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. Tests carried out for proteins of known structure indicate that the root-mean-square difference between the output of TALOS and the X-ray derived backbone angles is about 15 degrees.
The changes in solute chemical shift between an isotropic and a liquid crystalline phase provide information on the magnitude and orientation of the chemical shift anisotropy (CSA) tensor relative to the molecule’s alignment tensor (determined from the observed dipolar couplings and their known orientation in the three-dimensional structure of the molecule). Assuming all atoms of a given type have the same CSA tensor, the magnitude and orientation of the average 13C’, 15N and HN CSA tensors were determined. For HN, the scatter is completely dominated by intrinsic variations in the CSA tensor at the different sites. The degree of correlation between observed and predicted variations in 13C’ or 15N chemical shifts is dominated by the uncertainty in the protein structure and can be used as a sensitive monitor for evaluating the quality of that structure, or alternatively the difference between observed and predicted 13C’ or 15N chemical shift variations can be used as a driving force in calculating the protein’s structure.
It is demonstrated that scalar couplings between a hydrogen bond donating 15N nucleus and a hydrogen bond accepting C=O group can readily be observed in uniformly 13C/15N-enriched ubiquitin. Over the small range of N-O hydrogen bond lengths (2.8-3.3 Angstrom) for which 3hJNC’ couplings are observable, the measured 3hJNC’ values in a binding domain of Streptococcal protein G can be fit to: 3hJNC’ = -59000 exp(-4RNO) +/- 0.09 Hz, or RNO = 2.75 – 0.25 ln(-3hJNC’) +/- 0.06 Angstrom. The sign of 3hJNC’, determined from a zero-quantum/double-quantum experiment, is found to be the same as that of the 1JNH coupling, i.e. negative.
One-bond 1JCaCb scalar couplings, measured in ubiquitin, exhibit a strong dependence on the local backbone conformation. Empirically, the deviation from the 1JCaCb value measured in the corresponding free amino acid, can be expressed as delta(1JCaCb) = 1.3 + 0.6 cos(psi-61°) + 2.2 cos[2(psi-61°)] – 0.9 cos[2(phi + 20°)] +/- 0.5 Hz, where phi and psi are the intraresidue polypeptide backbone torsion angles obtained from ubiquitin’s X-ray structure. The relation between 1JCaCb and backbone torsion angles is confirmed by density functional theory (DFT) calculations on the peptide analog Ace-Ala-NMe.

Cuvinte cheie: structura, proteine, rezonanta magnetica nucleara, RMN, legaturi de hidrogen, tensor de anisotropie a deplasarii chimice // NMR, protein structure, chemical shift, CSA, hydrogen bond

URL: http://wwwlib.umi.com/dxweb/gateway