Literature DB >> 15140445

Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF.

Olivier Walker1, Ranjani Varadan, David Fushman.   

Abstract

We present a computer program ROTDIF for efficient determination of a complete rotational diffusion tensor of a molecule from NMR relaxation data. The derivation of the rotational diffusion tensor in the case of a fully anisotropic model is based on a six-dimensional search, which could be very time consuming, particularly if a grid search in the Euler angle space is involved. Here, we use an efficient Levenberg-Marquardt algorithm combined with Monte Carlo generation of initial guesses. The result is a dramatic, up to 50-fold improvement in the computational efficiency over the previous approaches. This method is demonstrated on a computer-generated and real protein systems. We also address the issue of sensitivity of the diffusion tensor determination from (15)N relaxation measurements to experimental errors in the relaxation rates and discuss possible artifacts from applying higher-symmetry tensor model and how to recognize them.

Mesh:

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Year:  2004        PMID: 15140445     DOI: 10.1016/j.jmr.2004.03.019

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  36 in total

1.  Determining protein dynamics from ¹⁵N relaxation data by using DYNAMICS.

Authors:  David Fushman
Journal:  Methods Mol Biol       Date:  2012

2.  Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell-mimicking crowded solution.

Authors:  Francesca Munari; Andrea Bortot; Serena Zanzoni; Mariapina D'Onofrio; David Fushman; Michael Assfalg
Journal:  FEBS Lett       Date:  2017-03-19       Impact factor: 4.124

3.  Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters.

Authors:  Jennifer B Hall; David Fushman
Journal:  J Am Chem Soc       Date:  2006-06-21       Impact factor: 15.419

4.  Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

Authors:  Yaroslav Ryabov; David Fushman
Journal:  J Am Chem Soc       Date:  2007-06-06       Impact factor: 15.419

5.  Compensatory and long-range changes in picosecond-nanosecond main-chain dynamics upon complex formation: 15N relaxation analysis of the free and bound states of the ubiquitin-like domain of human plexin-B1 and the small GTPase Rac1.

Authors:  S Bouguet-Bonnet; M Buck
Journal:  J Mol Biol       Date:  2008-02-04       Impact factor: 5.469

6.  Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

Authors:  Konstantin Berlin; Andrew Longhini; T Kwaku Dayie; David Fushman
Journal:  J Biomol NMR       Date:  2013-10-30       Impact factor: 2.835

Review 7.  Equivalence between Euler angle conventions for the description of tensorial interactions in liquid NMR: application to different software programs.

Authors:  Patrice Dosset; Philippe Barthe; Martin Cohen-Gonsaud; Christian Roumestand; Hélène Déméné
Journal:  J Biomol NMR       Date:  2013-10-17       Impact factor: 2.835

8.  Functional dynamics in replication protein A DNA binding and protein recruitment domains.

Authors:  Chris A Brosey; Sarah E Soss; Sonja Brooks; Chunli Yan; Ivaylo Ivanov; Kavita Dorai; Walter J Chazin
Journal:  Structure       Date:  2015-05-21       Impact factor: 5.006

9.  Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin.

Authors:  Priya R Banerjee; Shadakshara S Puttamadappa; Ajay Pande; Alexander Shekhtman; Jayanti Pande
Journal:  J Mol Biol       Date:  2011-07-30       Impact factor: 5.469

10.  Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication.

Authors:  Andrew C Goodrich; David J Meyers; Dominique P Frueh
Journal:  J Biol Chem       Date:  2017-04-28       Impact factor: 5.157

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