Investigation of the neighboring residue effects on protein chemical shifts

被引:90
作者
Wang, YJ [1 ]
Jardetzky, O [1 ]
机构
[1] Stanford Univ, Dept Mol Pharmacol, Stanford, CA 94305 USA
关键词
D O I
10.1021/ja026811f
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
In this study, we report nearest neighbor residue effects statistically determined from a chemical shift database. For an amino acid sequence XYZ, we define two correction factors, Delta(Y-x)n,s and Delta(Y-z)n,s, representing the effects on Y's chemical shifts from the preceding residue (X) and the following residue (Z), respectively, where X, Y, and Z are any of the 20 naturally occurring amino acids, n stands for H-1(N), N-15, H-1(alpha), C-13(alpha), C-13(beta), and C-13' nuclei, and s represents the three secondary structural types beta-strand, random coil, and alpha-helix. A total of similar to14400 Delta(Y-x)n,s and Delta(Y-z)n,s, representing nearly all combinations of X, Y, Z, n, and s, have been quantitatively determined. Our approach overcomes the limits of earlier experimental methods using short model peptides, and the resulting correction factors have important applications such as chemical shift prediction for the folded proteins. More importantly, we have found, for the first time, a linear correlation between the Delta(Y-x)n,s (n = N-15) and the C-13(alpha) chemical shifts of the preceding residue X. Since C-13(alpha) chemical shifts of the 20 amino acids, which span a wide range of 40-70 ppm, are largely dominated by one property, the electron density of the side chain, the correlation indicates that the same property is responsible for the effect on the following residue. The influence of the secondary structure on both the chemical shifts and the nearest neighbor residue effect are also investigated.
引用
收藏
页码:14075 / 14084
页数:10
相关论文
共 34 条
[1]   Helix capping [J].
Aurora, R ;
Rose, GD .
PROTEIN SCIENCE, 1998, 7 (01) :21-38
[2]   Protein phi and psi dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures [J].
Beger, RD ;
Bolton, PH .
JOURNAL OF BIOMOLECULAR NMR, 1997, 10 (02) :129-142
[3]   SEQUENCE-CORRECTED N-15 RANDOM COIL CHEMICAL-SHIFTS [J].
BRAUN, D ;
WIDER, G ;
WUTHRICH, K .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (19) :8466-8469
[5]   Protein backbone angle restraints from searching a database for chemical shift and sequence homology [J].
Cornilescu, G ;
Delaglio, F ;
Bax, A .
JOURNAL OF BIOMOLECULAR NMR, 1999, 13 (03) :289-302
[6]   N-15 CHEMICAL-SHIFTS OF BACKBONE AMIDES IN BOVINE PANCREATIC TRYPSIN-INHIBITOR AND APAMIN [J].
GLUSHKA, J ;
LEE, M ;
COFFIN, S ;
COWBURN, D .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1989, 111 (20) :7716-7722
[7]  
GRONENBORN AM, 1994, J BIOMOL NMR, V4, P455
[8]   Cα and Cβ carbon-13 chemical shifts in proteins from an empirical database [J].
Iwadate, M ;
Asakura, T ;
Williamson, MP .
JOURNAL OF BIOMOLECULAR NMR, 1999, 13 (03) :199-211
[9]   DICTIONARY OF PROTEIN SECONDARY STRUCTURE - PATTERN-RECOGNITION OF HYDROGEN-BONDED AND GEOMETRICAL FEATURES [J].
KABSCH, W ;
SANDER, C .
BIOPOLYMERS, 1983, 22 (12) :2577-2637
[10]   THERMODYNAMIC BETA-SHEET PROPENSITIES MEASURED USING A ZINC-FINGER HOST PEPTIDE [J].
KIM, CWA ;
BERG, JM .
NATURE, 1993, 362 (6417) :267-270