Nonuniform sampling and maximum entropy reconstruction applied to the accurate measurement of residual dipolar couplings

被引:17
作者
Kubat, Jayne A.
Chou, James J.
Rovnyak, David [1 ]
机构
[1] Bucknell Univ, Dept Chem, Lewisburg, PA 17837 USA
[2] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
关键词
residual dipolar coupling; maximum entropy reconstruction; nonuniform sampling; calmodulin;
D O I
10.1016/j.jmr.2007.01.022
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Residual dipolar couplings (RDC) provide important global restraints for accurate structure determination by NMR. We show that nonuniform sampling in combination with maximum entropy reconstruction (MaxEnt) is a promising strategy for accelerating and potentially enhancing the acquisition of RDC spectra. Using MaxEnt-processed spectra of nonuniformly sampled data sets that are reduced up to one fifth relative to uniform sampling, accurate C-13'-C-13(alpha) RDCs can be obtained that agree with an RMS of 0.67 Hz with those derived from uniformly sampled, Fourier transformed spectra. While confirming that frequency errors in MaxEnt spectra are very slight, an unexpected class of systematic errors was found to occur in the 6th significant figure of C-13' chemical shifts of doublets obtained by MaxEnt reconstruction. We show that this error stems from slight line shape perturbations and predict it should be encountered in other nonlinear spectral estimation algorithms. In the case of MaxEnt reconstruction, the error can easily be rendered systematic by straightforward optimization of MaxEnt reconstruction parameters and self-cancels in obtaining RDCs from nominiformly sampled, MaxEnt reconstructed spectra. (c) 2007 Elsevier Inc. All rights reserved.
引用
收藏
页码:201 / 211
页数:11
相关论文
共 45 条
[1]   The extended fourier transform for 2D spectral estimation [J].
Armstrong, GS ;
Mandelshtam, VA .
JOURNAL OF MAGNETIC RESONANCE, 2001, 153 (01) :22-31
[2]   THE ACCORDION EXPERIMENT, A SIMPLE APPROACH TO 3-DIMENSIONAL NMR-SPECTROSCOPY [J].
BODENHAUSEN, G ;
ERNST, RR .
JOURNAL OF MAGNETIC RESONANCE, 1981, 45 (02) :367-373
[3]   Theory of covariance nuclear magnetic resonance spectroscopy [J].
Brüschweiler, R .
JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (01) :409-414
[4]   Covariance nuclear magnetic resonance spectroscopy [J].
Brüschweiler, R ;
Zhang, FL .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (11) :5253-5260
[5]   RRT: The regularized resolvent transform for high-resolution spectral estimation [J].
Chen, JH ;
Shaka, AJ ;
Mandelshtam, VA .
JOURNAL OF MAGNETIC RESONANCE, 2000, 147 (01) :129-137
[6]   Ultra-high resolution 3D NMR spectra from limited-size data sets [J].
Chen, JH ;
Nietlispach, D ;
Shaka, AJ ;
Mandelshtam, VA .
JOURNAL OF MAGNETIC RESONANCE, 2004, 169 (02) :215-224
[7]   Measurement of one-bond 15N-13C′ dipolar couplings in medium sized proteins [J].
Chou, JJ ;
Delaglio, F ;
Bax, A .
JOURNAL OF BIOMOLECULAR NMR, 2000, 18 (02) :101-105
[8]   Generalized reconstruction of n-D NMR spectra from multiple projections:: Application to the 5-D HACACONH spectrum of protein G B1 domain [J].
Coggins, BE ;
Venters, RA ;
Zhou, P .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (04) :1000-1001
[9]   MAXIMUM-ENTROPY AND NMR - A NEW APPROACH [J].
DANIELL, GJ ;
HORE, PJ .
JOURNAL OF MAGNETIC RESONANCE, 1989, 84 (03) :515-536
[10]   NMRPIPE - A MULTIDIMENSIONAL SPECTRAL PROCESSING SYSTEM BASED ON UNIX PIPES [J].
DELAGLIO, F ;
GRZESIEK, S ;
VUISTER, GW ;
ZHU, G ;
PFEIFER, J ;
BAX, A .
JOURNAL OF BIOMOLECULAR NMR, 1995, 6 (03) :277-293