Literature DB >> 10718609

Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data.

P Dosset1, J C Hus, M Blackledge, D Marion.   

Abstract

A novel program has been developed for the interpretation of 15N relaxation rates in terms of macromolecular anisotropic rotational diffusion. The program is based on a highly efficient simulated annealing/minimization algorithm, designed specifically to search the parametric space described by the isotropic, axially symmetric and fully anisotropic rotational diffusion tensor models. The high efficiency of this algorithm allows extensive noise-based Monte Carlo error analysis. Relevant statistical tests are systematically applied to provide confidence limits for the proposed tensorial models. The program is illustrated here using the example of the cytochrome c' from Rhodobacter capsulatus, a four-helix bundle heme protein, for which data at three different field strengths were independently analysed and compared.

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Year:  2000        PMID: 10718609     DOI: 10.1023/a:1008305808620

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  10 in total

Review 1.  Probing molecular motion by NMR.

Authors:  A G Palmer
Journal:  Curr Opin Struct Biol       Date:  1997-10       Impact factor: 6.809

2.  Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation.

Authors:  L K Lee; M Rance; W J Chazin; A G Palmer
Journal:  J Biomol NMR       Date:  1997-04       Impact factor: 2.835

Review 3.  Protein dynamics from NMR.

Authors:  L E Kay
Journal:  Nat Struct Biol       Date:  1998-07

4.  Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.

Authors:  N Tjandra; D S Garrett; A M Gronenborn; A Bax; G M Clore
Journal:  Nat Struct Biol       Date:  1997-06

5.  A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization.

Authors:  J M Schurr; H P Babcock; B S Fujimoto
Journal:  J Magn Reson B       Date:  1994-11

6.  High-resolution crystal structures of two polymorphs of cytochrome c' from the purple phototrophic bacterium rhodobacter capsulatus.

Authors:  T H Tahirov; S Misaki; T E Meyer; M A Cusanovich; Y Higuchi; N Yasuoka
Journal:  J Mol Biol       Date:  1996-06-14       Impact factor: 5.469

7.  The effect of noncollinearity of 15N-1H dipolar and 15N CSA tensors and rotational anisotropy on 15N relaxation, CSA/dipolar cross correlation, and TROSY.

Authors:  D Fushman; D Cowburn
Journal:  J Biomol NMR       Date:  1999-02       Impact factor: 2.835

8.  Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling.

Authors:  R Brüschweiler; X Liao; P E Wright
Journal:  Science       Date:  1995-05-12       Impact factor: 47.728

9.  Solution structure, rotational diffusion anisotropy and local backbone dynamics of Rhodobacter capsulatus cytochrome c2.

Authors:  F Cordier; M Caffrey; B Brutscher; M A Cusanovich; D Marion; M Blackledge
Journal:  J Mol Biol       Date:  1998-08-14       Impact factor: 5.469

10.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

  10 in total
  190 in total

1.  Solution structure of the viral receptor domain of Tva and its implications in viral entry.

Authors:  Qing-Yin Wang; Wen Huang; Klavs Dolmer; Peter G W Gettins; Lijun Rong
Journal:  J Virol       Date:  2002-03       Impact factor: 5.103

2.  Backbone dynamics of the regulatory domain of calcium vector protein, studied by (15)N relaxation at four fields, reveals unique mobility characteristics of the intermotif linker.

Authors:  I Théret; J A Cox; J Mispelter; C T Craescu
Journal:  Protein Sci       Date:  2001-07       Impact factor: 6.725

3.  A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

Authors:  P Dosset; J C Hus; D Marion; M Blackledge
Journal:  J Biomol NMR       Date:  2001-07       Impact factor: 2.835

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

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

5.  Solution structure, dynamics and thermodynamics of the three SH3 domains of CD2AP.

Authors:  Jose L Ortega Roldan; Martin Blackledge; Nico A J van Nuland; Ana I Azuaga
Journal:  J Biomol NMR       Date:  2011-04-26       Impact factor: 2.835

6.  FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data.

Authors:  Roger Cole; J Patrick Loria
Journal:  J Biomol NMR       Date:  2003-07       Impact factor: 2.835

7.  Solution structure of Ca2+-free rat beta-parvalbumin (oncomodulin).

Authors:  Michael T Henzl; John J Tanner
Journal:  Protein Sci       Date:  2007-09       Impact factor: 6.725

8.  Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors.

Authors:  Luis A Alcaraz; Lucia Banci; Ivano Bertini; Francesca Cantini; Antonio Donaire; Leonardo Gonnelli
Journal:  J Biol Inorg Chem       Date:  2007-08-21       Impact factor: 3.358

9.  NMR study of general anesthetic interaction with nAChR beta2 subunit.

Authors:  Vasyl Bondarenko; Victor E Yushmanov; Yan Xu; Pei Tang
Journal:  Biophys J       Date:  2007-11-09       Impact factor: 4.033

10.  Interdomain tilt angle determines integrin-dependent function of the ninth and tenth FIII domains of human fibronectin.

Authors:  Harri Altroff; Robin Schlinkert; Christopher F van der Walle; Andrea Bernini; Iain D Campbell; Jörn M Werner; Helen J Mardon
Journal:  J Biol Chem       Date:  2004-10-12       Impact factor: 5.157

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