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The weight of a particular secondary shift was adjusted by considering the width of its distribution over a narrow range of backbone torsion angles relative to the entire range of secondary chemical shifts in the database

Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Journal of biomolecular NMR, no. 3 (1999): 289-302

Cited: 3155|Views27

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φ angleΨ anglebackbone angleschemical shifthomology of chemical shiftMore(3+)

Abstract

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide th...More

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Introduction

The strong dependence of isotropic chemical shifts on protein structure has long been recognized.
The striking correlation between 1Hα chemical shift and secondary structure has been studied extensively (Pastore and Saudek, 1990; Williamson, 1990; Wishart et al, 1991; Ösapay and Case, 1994) and the 1HN shift was found to be sensitive to both hydrogen bonding and secondary structure (Pardi et al, 1983; Williamson, 1990; Wishart et al, 1991).
The secondary 13Cα and 13Cβ chemical shifts of a given residue were found to correlate closely with its φ and torsion angles (Ando et al, 1984; Saito, 1986; Spera and Bax, 1991), and thereby with secondary structure (Wishart et al, 1991)

Highlights

The strong dependence of isotropic chemical shifts on protein structure has long been recognized
Rather than relying on the information supplied with the deposited chemical shift data, we evaluate the need for applying a correction to 13C shifts by calculating how much, on average, the secondary shifts deviate from the corresponding secondary chemical shifts predicted by the (φ, )-surfaces of Spera and Bax
An outline of the prediction method used by TALOS is presented in Figure 1
TALOS evaluates the similarity in amino acid sequence and secondary shifts for a string of three sequential amino acids relative to all triplets of sequential residues contained in the database
The approach described in this paper is the first to combine both chemical shift and residue type information for predicting backbone torsion angles
The weight of a particular secondary shift was adjusted by considering the width of its distribution over a narrow range of backbone torsion angles relative to the entire range of secondary chemical shifts in the database

Methods

A database was created which contains nearly complete 13Cα, 13Cβ, 13C , 1Hα and 15N chemical shift assignments of 20 proteins (Table 1), together with the backbone torsion angles φ and , derived from crystal structures solved at a resolution ≤ 2.2 Å.
Residues with high temperature (B) factors for the backbone atoms, exceeding 1.5 times the average B-factor for that protein, were excluded
This includes the vast majority of cases where differences between crystal and solution structures previously have been noted

Results

Description of the search procedure The backbone torsion angle prediction package TALOS (Torsion Angle Likelihood Obtained from Shifts and sequence similarity) is written in the Tcl/Tk language (Ousterhout, 1994) and uses NMRWish, a companion package to the NMRPipe processing and analysis system (Delaglio et al, 1995).
TALOS evaluates the similarity in amino acid sequence and secondary shifts for a string of three sequential amino acids relative to all triplets of sequential residues contained in the database.
For each query triplet of consecutive residues, the similarity to a triplet with center-residue j in the database is evaluated by computing a similarity factor, S(i, j ), given by:

Conclusion

The approach described in this paper is the first to combine both chemical shift and residue type information for predicting backbone torsion angles.
The weight of a particular secondary shift was adjusted by considering the width of its distribution over a narrow range of backbone torsion angles relative to the entire range of secondary chemical shifts in the database.
The relative importance of the chemical shifts versus residue homology has been adjusted empirically to yield the most reliable predictions for proteins of known structure.
Reliability of TALOS predictions is considerably improved when including this residue type homology

Tables

Table1: Proteins contained in the database
Table2: Empirically optimized k factors, kmn (m: homology, Cα, N, Cβ, C , Hα; n = −1, 0, 1), for weighting the relative importance of a given chemical shift or residue type in determining the similarity score, S(i, j ) of Equation 1
Table3: Residue similarity factors, ResType, used by TALOS in Equation 1
Table4: Summary of TALOS results when applied to predicting backbone angles of proteins included in the database

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Funding

Evaluates the need for applying a correction to 13C shifts by calculating how much, on average, the secondary shifts deviate from the corresponding secondary chemical shifts predicted by the -surfaces of Spera and Bax

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F Delaglio

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A Bax

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