Self-Consistent Karplus Parametrization of 3J Couplings Depending on the Polypeptide Side-Chain Torsion 1
详细信息 查看全文
- 作者：Carlos Pé ; rez ; Frank Lö ; hr ; Heinz Rü ; terjans ; and Jü ; rgen M. Schmidt
- 刊名：Journal of the American Chemical Society
- 出版年：2001
- 出版时间：July 25, 2001
- 年：2001
- 卷：123
- 期：29
- 页码：7081 - 7093
- 全文大小：154K
- 年卷期：v.123,no.29(July 25, 2001)
- ISSN：1520-5126
文摘
Recently proposed self-consistent 3J coupling analysis (Schmidt, J. M.; Blümel, M.; Löhr, F.;Rüterjans, H. J. Biomol. NMR 1999, 14, 1-12) has been carried out to calibrate Karplus parameters constitutingthe empirical dependence of 3J coupling constants on the 
fchars/chi.gif" BORDER=0 >1 dihedral angle in amino acid side chains. Theprocedure involves simultaneous least-squares optimization of six sets of three Karplus coefficients related toall six 3J coupling types accessible in 15N,13C-labeled proteins. A simple concept of fundamental and incrementalcomponent couplings is proposed to account for substituent effects, eventually yielding amino acid topology-specific Karplus parameters. The method is exemplified with recombinant Desulfovibrio vulgaris flavodoxin(147 amino acids, 16 kDa) with reference to a total of 749 experimental 3JHfchars/alpha.gif" BORDER=0>,Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JN',Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JC',Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JHfchars/alpha.gif" BORDER=0>,Cfchars/gamma.gif" BORDER=0 >, 3JN',Cfchars/gamma.gif" BORDER=0 >,and 3JC',Cfchars/gamma.gif" BORDER=0 > coupling constants. Unlike other parametrizations, the present method does not make reference toX-ray coordinates, so that the Karplus coefficients obtained are not influenced by differences between solutionand crystal states. Cross validation using X-ray torsion angles demonstrates the improvement relative to previousparametrizations. The Karplus coefficients derived are applicable to other proteins, too. Parameter refinementalso yields a series of fchars/chi.gif" BORDER=0 >1 torsion angles, providing valuable constraints for protein structure determination, aswell as optional parameters of local angular mobility in the contexts of Gaussian random fluctuation or athree-site jump model. The procedure permits automatic stereospecific assignments of Hfchars/beta2.gif" BORDER=0 ALIGN="middle"> and Cfchars/gamma.gif" BORDER=0 > chemicalshifts. The majority of the flavodoxin side-chain conformations agrees with high-resolution X-ray structuresof the protein. Marked deviations between NMR and X-ray datasets are attributed to different rotameric statesdue to crystal-packing effects and to conformational equilibria between multiple fchars/chi.gif" BORDER=0 >1 rotamers.
fchars/chi.gif" BORDER=0 >1 dihedral angle in amino acid side chains. Theprocedure involves simultaneous least-squares optimization of six sets of three Karplus coefficients related toall six 3J coupling types accessible in 15N,13C-labeled proteins. A simple concept of fundamental and incrementalcomponent couplings is proposed to account for substituent effects, eventually yielding amino acid topology-specific Karplus parameters. The method is exemplified with recombinant Desulfovibrio vulgaris flavodoxin(147 amino acids, 16 kDa) with reference to a total of 749 experimental 3JHfchars/alpha.gif" BORDER=0>,Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JN',Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JC',Hfchars/beta2.gif" BORDER=0 ALIGN="middle">, 3JHfchars/alpha.gif" BORDER=0>,Cfchars/gamma.gif" BORDER=0 >, 3JN',Cfchars/gamma.gif" BORDER=0 >,and 3JC',Cfchars/gamma.gif" BORDER=0 > coupling constants. Unlike other parametrizations, the present method does not make reference toX-ray coordinates, so that the Karplus coefficients obtained are not influenced by differences between solutionand crystal states. Cross validation using X-ray torsion angles demonstrates the improvement relative to previousparametrizations. The Karplus coefficients derived are applicable to other proteins, too. Parameter refinementalso yields a series of fchars/chi.gif" BORDER=0 >1 torsion angles, providing valuable constraints for protein structure determination, aswell as optional parameters of local angular mobility in the contexts of Gaussian random fluctuation or athree-site jump model. The procedure permits automatic stereospecific assignments of Hfchars/beta2.gif" BORDER=0 ALIGN="middle"> and Cfchars/gamma.gif" BORDER=0 > chemicalshifts. The majority of the flavodoxin side-chain conformations agrees with high-resolution X-ray structuresof the protein. Marked deviations between NMR and X-ray datasets are attributed to different rotameric statesdue to crystal-packing effects and to conformational equilibria between multiple fchars/chi.gif" BORDER=0 >1 rotamers.