Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data

被引:40
作者
d'Auvergne, Edward J. [1 ]
Gooley, Paul R. [1 ]
机构
[1] Univ Melbourne, Dept Biochem & Mol Biol, Bio21 Inst Biotechnol & Mol Sci, Parkville, Vic 3010, Australia
关键词
data analysis; error analysis; mathematical modelling; model-free analysis; model elimination; model selection; model validation; NMR relaxation;
D O I
10.1007/s10858-006-9007-z
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
Model-free analysis is a technique commonly used within the field of NMR spectroscopy to extract atomic resolution, interpretable dynamic information on multiple timescales from the R (1), R (2), and steady state NOE. Model-free approaches employ two disparate areas of data analysis, the discipline of mathematical optimisation, specifically the minimisation of a chi(2) function, and the statistical field of model selection. By searching through a large number of model-free minimisations, which were setup using synthetic relaxation data whereby the true underlying dynamics is known, certain model-free models have been identified to, at times, fail. This has been characterised as either the internal correlation times, tau (e) , tau (f) , or tau (s) , or the global correlation time parameter, local tau (m) , heading towards infinity, the result being that the final parameter values are far from the true values. In a number of cases the minimised chi(2) value of the failed model is significantly lower than that of all other models and, hence, will be the model which is chosen by model selection techniques. If these models are not removed prior to model selection the final model-free results could be far from the truth. By implementing a series of empirical rules involving inequalities these models can be specifically isolated and removed. Model-free analysis should therefore consist of three distinct steps: model-free minimisation, model-free model elimination, and finally model-free model selection. Failure has also been identified to affect the individual Monte Carlo simulations used within error analysis. Each simulation involves an independent randomised relaxation data set and model-free minimisation, thus simulations suffer from exactly the same types of failure as model-free models. Therefore, to prevent these outliers from causing a significant overestimation of the errors the failed Monte Carlo simulations need to be culled prior to calculating the parameter standard deviations.
引用
收藏
页码:117 / 135
页数:19
相关论文
共 14 条
[1]   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
[2]  
BELLOMO N, 1994, MODELLING MATH METHO
[3]   Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation [J].
Chen, JH ;
Brooks, CL ;
Wright, PE .
JOURNAL OF BIOMOLECULAR NMR, 2004, 29 (03) :243-257
[4]   DEVIATIONS FROM THE SIMPLE 2-PARAMETER MODEL-FREE APPROACH TO THE INTERPRETATION OF N-15 NUCLEAR MAGNETIC-RELAXATION OF PROTEINS [J].
CLORE, GM ;
SZABO, A ;
BAX, A ;
KAY, LE ;
DRISCOLL, PC ;
GRONENBORN, AM .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1990, 112 (12) :4989-4991
[5]   The use of model selection in the model-free analysis of protein dynamics [J].
d'Auvergne, EJ ;
Gooley, PR .
JOURNAL OF BIOMOLECULAR NMR, 2003, 25 (01) :25-39
[6]   The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: Analysis of N-15 relaxation with monomer/dimer equilibration [J].
Fushman, D ;
Cahill, S ;
Cowburn, D .
JOURNAL OF MOLECULAR BIOLOGY, 1997, 266 (01) :173-194
[7]   NMR studies of Brownian tumbling and internal motions in proteins [J].
Korzhnev, DM ;
Billeter, M ;
Arseniev, AS ;
Orekhov, VY .
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 2001, 38 (03) :197-266
[8]   MODEL-FREE APPROACH TO THE INTERPRETATION OF NUCLEAR MAGNETIC-RESONANCE RELAXATION IN MACROMOLECULES .2. ANALYSIS OF EXPERIMENTAL RESULTS [J].
LIPARI, G ;
SZABO, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1982, 104 (17) :4559-4570
[9]   MODEL-FREE APPROACH TO THE INTERPRETATION OF NUCLEAR MAGNETIC-RESONANCE RELAXATION IN MACROMOLECULES .1. THEORY AND RANGE OF VALIDITY [J].
LIPARI, G ;
SZABO, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1982, 104 (17) :4546-4559
[10]   BACKBONE DYNAMICS OF ESCHERICHIA-COLI RIBONUCLEASE HI - CORRELATIONS WITH STRUCTURE AND FUNCTION IN AN ACTIVE ENZYME [J].
MANDEL, AM ;
AKKE, M ;
PALMER, AG .
JOURNAL OF MOLECULAR BIOLOGY, 1995, 246 (01) :144-163