A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data

被引:16
作者
Andrec, M
Inman, KG
Weber, DJ
Levy, RM
Montelione, GT
机构
[1] Rutgers State Univ, Dept Chem, Wright Rieman Labs, Piscataway, NJ 08855 USA
[2] Rutgers State Univ, Ctr Adv Biotechnol & Med, Piscataway, NJ 08855 USA
[3] Rutgers State Univ, Dept Mol Biol & Biochem, Piscataway, NJ 08855 USA
[4] Univ Maryland, Sch Med, Dept Biol Chem, Baltimore, MD 21201 USA
基金
美国国家卫生研究院;
关键词
backbone dynamics; Lipari-Szabo formalism; rotational correlation time; Monte Carlo; multiple fields; chemical exchange;
D O I
10.1006/jmre.2000.2113
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
It has recently become more widely appreciated that the presence of rotational diffusional anisotropy in proteins and other macromolecules can have a significant affect on the interpretation of NMR relaxation data in terms of molecular motion. In this paper, we show how commonly used NMR relaxation data (R-1, R-2, and NOE) obtained at two spectrometer frequencies can be analyzed using a Bayesian statistical approach to reliably detect and quantify the degree of rotational diffusion anisotropy. Our approach differs from previous methods in that it does not make assumptions concerning the internal motions experienced by the residues which are used to quantify the diffusion anisotropy, but rather averages the results over all internal motions consistent with the data. We demonstrate our method using synthetic data corresponding to isotropic, axially symmetric anisotropic, and fully asymmetric anisotropic rotational diffusion, as well as experimental NMR data. We compare the Bayesian statistical approach with a widely used method for extracting tumbling parameters using both synthetic and experimental data. While it can be difficult to separate the effects of chemical exchange from rotational anisotropy using this "standard" method, these effects are readily separated using Bayesian statistics. In addition, we find that the Bayesian statistical approach requires considerably less CPU time than an equivalent standard analysis. (C) 2000 Academic Press.
引用
收藏
页码:66 / 80
页数:15
相关论文
共 35 条
[1]   Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain [J].
Akke, M ;
Liu, J ;
Cavanagh, J ;
Erickson, HP ;
Palmer, AG .
NATURE STRUCTURAL BIOLOGY, 1998, 5 (01) :55-59
[2]   Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods [J].
Andrec, M ;
Montelione, GT ;
Levy, RM .
JOURNAL OF MAGNETIC RESONANCE, 1999, 139 (02) :408-421
[3]   BACKBONE DYNAMICS OF CALMODULIN STUDIED BY N-15 RELAXATION USING INVERSE DETECTED 2-DIMENSIONAL NMR-SPECTROSCOPY - THE CENTRAL HELIX IS FLEXIBLE [J].
BARBATO, G ;
IKURA, M ;
KAY, LE ;
PASTOR, RW ;
BAX, A .
BIOCHEMISTRY, 1992, 31 (23) :5269-5278
[4]   Precision and uncertainty in the characterization of anisotropic rotational diffusion by 15N relaxation [J].
Blackledge, M ;
Cordier, F ;
Dosset, P ;
Marion, D .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (18) :4538-4539
[5]   Defining the orientation of the 15N shielding tensor using 15N NMR relaxation data for a protein in solution [J].
Boyd, J ;
Redfield, C .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (37) :9692-9693
[6]   LONG-RANGE MOTIONAL RESTRICTIONS IN A MULTIDOMAIN ZINC-FINGER PROTEIN FROM ANISOTROPIC TUMBLING [J].
BRUSCHWEILER, R ;
LIAO, XB ;
WRIGHT, PE .
SCIENCE, 1995, 268 (5212) :886-889
[7]   The use of residual dipolar coupling in concert with backbone relaxation rates to identify conformational exchange by NMR [J].
de Alba, E ;
Baber, JL ;
Tjandra, N .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (17) :4282-4283
[8]   Solution structure of rat apo-S100B(beta beta) as determined by NMR spectroscopy [J].
Drohat, AC ;
Amburgey, JC ;
Abildgaard, F ;
Starich, MR ;
Baldisseri, D ;
Weber, DJ .
BIOCHEMISTRY, 1996, 35 (36) :11577-11588
[9]  
Drohat AC, 1999, PROTEIN SCI, V8, P800
[10]   Protein NMR relaxation: theory, applications and outlook [J].
Fischer, MWF ;
Majumdar, A ;
Zuiderweg, ERP .
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 1998, 33 :207-272