Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data
- 22 June 2006
- journal article
- Published by Springer Nature in Journal of Biomolecular NMR
- Vol. 35 (2) , 117-135
- https://doi.org/10.1007/s10858-006-9007-z
Abstract
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 χ2 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, τ e , τ f , or τ s , or the global correlation time parameter, local τ 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 χ2 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.Keywords
This publication has 13 references indexed in Scilit:
- Model-free Analysis of Protein Dynamics: Assessment of Accuracy and Model Selection Protocols Based on Molecular Dynamics SimulationJournal of Biomolecular NMR, 2004
- The use of model selection in the model-free analysis of protein dynamics.Journal of Biomolecular NMR, 2003
- NMR studies of Brownian tumbling and internal motions in proteinsProgress in Nuclear Magnetic Resonance Spectroscopy, 2001
- Estimation of Dynamic Parameters from NMR Relaxation Data using the Lipari–Szabo Model-Free Approach and Bayesian Statistical MethodsJournal of Magnetic Resonance, 1999
- 1H-15N NMR dynamic study of an isolated α-helical peptide (1–36)- bacteriorhodopsin reveals the equilibrium helix-coil transitionsJournal of Biomolecular NMR, 1999
- The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibrationJournal of Molecular Biology, 1997
- Backbone Dynamics of Ribonuclease HI: Correlations with Structure and Function in an Active EnzymeJournal of Molecular Biology, 1995
- Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteinsJournal of the American Chemical Society, 1990
- Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental resultsJournal of the American Chemical Society, 1982
- Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validityJournal of the American Chemical Society, 1982