Literature DB >> 8720833

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

A M Bonvin1, A T Brünger.   

Abstract

The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.

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Year:  1996        PMID: 8720833     DOI: 10.1007/BF00190458

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


  19 in total

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Authors:  Y Kim; J H Prestegard
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2.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.

Authors:  P Gros; W F van Gunsteren; W G Hol
Journal:  Science       Date:  1990-09-07       Impact factor: 47.728

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Authors:  M Nilges; G M Clore; A M Gronenborn
Journal:  FEBS Lett       Date:  1988-03-14       Impact factor: 4.124

4.  A dynamic model for the structure of acyl carrier protein in solution.

Authors:  Y Kim; J H Prestegard
Journal:  Biochemistry       Date:  1989-10-31       Impact factor: 3.162

5.  Structure refinement using time-averaged J-coupling constant restraints.

Authors:  A E Torda; R M Brunne; T Huber; H Kessler; W F van Gunsteren
Journal:  J Biomol NMR       Date:  1993-01       Impact factor: 2.835

6.  Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.

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Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

7.  Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.

Authors:  F T Burling; W I Weis; K M Flaherty; A T Brünger
Journal:  Science       Date:  1996-01-05       Impact factor: 47.728

8.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
Journal:  Science       Date:  1993-07-16       Impact factor: 47.728

9.  Multiconformational analysis of solution NOE data for the Ac-(L)proline-(D)alanine-NHMe dipeptide in a nonprotic solvent.

Authors:  C R Landis; L L Luck; J M Wright
Journal:  J Magn Reson B       Date:  1995-10

10.  Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.

Authors:  P D Jeffrey; A A Russo; K Polyak; E Gibbs; J Hurwitz; J Massagué; N P Pavletich
Journal:  Nature       Date:  1995-07-27       Impact factor: 49.962

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  21 in total

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Journal:  J Biomol NMR       Date:  2000-02       Impact factor: 2.835

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Authors:  R Bürgi; J Pitera; W F van Gunsteren
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3.  FINGAR: A new genetic algorithm-based method for fitting NMR data.

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4.  Estimating the accuracy of protein structures using residual dipolar couplings.

Authors:  Katya Simon; Jun Xu; Chinpal Kim; Nikolai R Skrynnikov
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5.  Comparison of multiple crystal structures with NMR data for engrailed homeodomain.

Authors:  Tomasz L Religa
Journal:  J Biomol NMR       Date:  2008-02-15       Impact factor: 2.835

6.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

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7.  The dynamic NMR structure of the T psi C-loop: implications for the specificity of tRNA methylation.

Authors:  L J Yao; T L James; J T Kealey; D V Santi; U Schmitz
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8.  Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

Authors:  Y Khoo; A Singer; D Cowburn
Journal:  J Biomol NMR       Date:  2017-06-14       Impact factor: 2.835

9.  Average conformations determined from PRE data provide high-resolution maps of transient tertiary interactions in disordered proteins.

Authors:  Jordi Silvestre-Ryan; Carlos W Bertoncini; Robert Bryn Fenwick; Santiago Esteban-Martin; Xavier Salvatella
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10.  Enhancing the quality of protein conformation ensembles with relative populations.

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Journal:  J Biomol NMR       Date:  2014-02-12       Impact factor: 2.835

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