Evaluation of uncertainty in alignment tensors obtained from dipolar couplings

被引:117
作者
Zweckstetter, M
Bax, A
机构
[1] NIDDKD, Chem Phys Lab, NIH, Bethesda, MD 20892 USA
[2] Max Planck Inst Biophys Chem, D-37077 Gottingen, Germany
基金
美国国家卫生研究院;
关键词
alignment tensor; backbone dynamics; dipolar coupling; error analysis; liquid crystal; order matrix; protein structure determination; ubiquitin;
D O I
10.1023/A:1016316415261
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Residual dipolar couplings and their corresponding alignment tensors are useful for structural analysis of macromolecules. The error in an alignment tensor, derived from residual dipolar couplings on the basis of a known structure, is determined not only by the accuracy of the measured couplings but also by the uncertainty in the structure (structural noise). This dependence is evaluated quantitatively on the basis of simulated structures using Monte-Carlo type analyses. When large numbers of dipolar couplings are available, structural noise is found to result in a systematic underestimate of the magnitude of the alignment tensor. Particularly in cases where only few dipolar couplings are available, structural noise can cause significant errors in best-fitted alignment tensor values, making determination of the relative orientation of small fragments and evaluation of local backbone mobility from dipolar couplings difficult. An example for the protein ubiquitin demonstrates the inherent limitations in characterizing motions on the basis of local alignment tensor magnitudes.
引用
收藏
页码:127 / 137
页数:11
相关论文
共 30 条
[1]  
Almond A, 2001, J BIOMOL NMR, V20, P351
[2]   Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization [J].
Bewley, CA ;
Clore, GM .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (25) :6009-6016
[3]  
Bothner-By A. A., 1996, ENCY NUCL MAGNETIC R, P2932
[4]   Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization [J].
Clore, GM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (16) :9021-9025
[5]   R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures [J].
Clore, GM ;
Garrett, DS .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (39) :9008-9012
[6]   Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase [J].
Cornilescu, G ;
Marquardt, JL ;
Ottiger, M ;
Bax, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (27) :6836-6837
[7]   Protein structure determination using molecular fragment replacement and NMR dipolar couplings [J].
Delaglio, F ;
Kontaxis, G ;
Bax, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (09) :2142-2143
[8]   THE DOUBLE CUBIC LATTICE METHOD - EFFICIENT APPROACHES TO NUMERICAL-INTEGRATION OF SURFACE-AREA AND VOLUME AND TO DOT SURFACE CONTOURING OF MOLECULAR ASSEMBLIES [J].
EISENHABER, F ;
LIJNZAAD, P ;
ARGOS, P ;
SANDER, C ;
SCHARF, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (03) :273-284
[9]  
Emsley J. W., 1996, ENCY NUCL MAGNETIC R, P2788
[10]   Domain orientation and dynamics in multidomain proteins from residual dipolar couplings [J].
Fischer, MWF ;
Losonczi, JA ;
Weaver, JL ;
Prestegard, JH .
BIOCHEMISTRY, 1999, 38 (28) :9013-9022