Literature DB >> 17579774

Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm.

Edward J d'Auvergne1, Paul R Gooley.   

Abstract

Model-free analysis of NMR relaxation data, which describes the motion of individual atoms, is a problem intricately linked to the Brownian rotational diffusion of the macromolecule. The diffusion tensor parameters strongly influence the optimisation of the various model-free models and the subsequent model selection between them. Finding the optimal model of the dynamics of the system among the numerous diffusion and model-free models is hence quite complex. Using set theory, the entirety of this global problem has been encapsulated by the universal set Ll, and its resolution mathematically formulated as the universal solution Ll. Ever since the original Lipari and Szabo papers the model-free dynamics of a molecule has most often been solved by initially estimating the diffusion tensor. The model-free models which depend on the diffusion parameter values are then optimised and the best model is chosen to represent the dynamics of the residue. Finally, the global model of all diffusion and model-free parameters is optimised. These steps are repeated until convergence. For simplicity this approach to Ll will be labelled the diffusion seeded model-free paradigm. Although this technique suffers from a number of problems many have been solved. All aspects of the diffusion seeded paradigm and its consequences, together with a few alternatives to the paradigm, will be reviewed through the use of set notation.

Mesh:

Substances:

Year:  2007        PMID: 17579774     DOI: 10.1039/b702202f

Source DB:  PubMed          Journal:  Mol Biosyst        ISSN: 1742-2051


  11 in total

1.  TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance.

Authors:  Olivier Fisette; Sébastien Morin; Pierre-Yves Savard; Patrick Lagüe; Stéphane M Gagné
Journal:  Biophys J       Date:  2010-02-17       Impact factor: 4.033

2.  relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

Authors:  Michael Bieri; Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2011-05-27       Impact factor: 2.835

3.  Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core.

Authors:  Milan Zachrdla; Petr Padrta; Alžbeta Rabatinová; Hana Šanderová; Ivan Barvík; Libor Krásný; Lukáš Žídek
Journal:  J Biol Chem       Date:  2017-05-24       Impact factor: 5.157

4.  A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red.

Authors:  Nina Senutovitch; Robyn L Stanfield; Shantanu Bhattacharyya; Gordon S Rule; Ian A Wilson; Bruce A Armitage; Alan S Waggoner; Peter B Berget
Journal:  Biochemistry       Date:  2012-03-14       Impact factor: 3.162

5.  RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.

Authors:  Thomas Biedenbänder; Vanessa de Jesus; Martina Schmidt-Dengler; Mark Helm; Björn Corzilius; Boris Fürtig
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

6.  Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions.

Authors:  Douglas J Kojetin; Patrick D McLaughlin; Richele J Thompson; David Dubnau; Peter Prepiak; Mark Rance; John Cavanagh
Journal:  J Mol Biol       Date:  2009-01-30       Impact factor: 5.469

7.  Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2007-12-18       Impact factor: 2.835

8.  Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2007-12-18       Impact factor: 2.835

9.  Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1.

Authors:  Ian A Bennet; L David Finger; Nicola J Baxter; Benjamin Ambrose; Andrea M Hounslow; Mark J Thompson; Jack C Exell; Nur Nazihah B Md Shahari; Timothy D Craggs; Jonathan P Waltho; Jane A Grasby
Journal:  Nucleic Acids Res       Date:  2018-06-20       Impact factor: 16.971

10.  Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail.

Authors:  Jing Wang; Emma J Murphy; Jay C Nix; David N M Jones
Journal:  Sci Rep       Date:  2020-02-24       Impact factor: 4.379

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.