Literature DB >> 1841688

Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide.

R Brüschweiler1, M Blackledge, R R Ernst.   

Abstract

A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 10(3) and 10(7) s-1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T1 rho measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T1 rho relaxation rates found for the NH protons of Val1 and Phe6 can be explained by a dynamical exchange between two structures.

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Year:  1991        PMID： 1841688     DOI： 10.1007/bf01874565

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


  17 in total

1.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm.

Authors:  W Braun; N Go
Journal:  J Mol Biol       Date:  1985-12-05       Impact factor: 5.469

2.  Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

Authors:  A E Torda; R M Scheek; W F van Gunsteren
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

Review 3.  Intermediates in the folding reactions of small proteins.

Authors:  P S Kim; R L Baldwin
Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

4.  Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR.

Authors:  H Roder; G A Elöve; S W Englander
Journal:  Nature       Date:  1988-10-20       Impact factor: 49.962

5.  NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A.

Authors:  J B Udgaonkar; R L Baldwin
Journal:  Nature       Date:  1988-10-20       Impact factor: 49.962

6.  Antamanide. Relaxation study of conformational equilibria.

Authors:  W Burgermeister; T Wieland; R Winkler
Journal:  Eur J Biochem       Date:  1974-05-02

Review 7.  Time-resolved fluorescence of proteins.

Authors:  J M Beechem; L Brand
Journal:  Annu Rev Biochem       Date:  1985       Impact factor: 23.643

8.  Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons.

Authors:  H Roder; K Wüthrich
Journal:  Proteins       Date:  1986-09

9.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

Authors:  R Kaptein; E R Zuiderweg; R M Scheek; R Boelens; W F van Gunsteren
Journal:  J Mol Biol       Date:  1985-03-05       Impact factor: 5.469

Review 10.  Fluctuations in protein structure from X-ray diffraction.

Authors:  G A Petsko; D Ringe
Journal:  Annu Rev Biophys Bioeng       Date:  1984
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  32 in total

1.  CLOUDS, a protocol for deriving a molecular proton density via NMR.

Authors:  Alexander Grishaev; Miguel Llinás
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-14       Impact factor: 11.205

2.  FINGAR: A new genetic algorithm-based method for fitting NMR data.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1996-07       Impact factor: 2.835

3.  The Exact NOE as an Alternative in Ensemble Structure Determination.

Authors:  Beat Vögeli; Simon Olsson; Peter Güntert; Roland Riek
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

4.  On using oscillating time-dependent restraints in MD simulation.

Authors:  Bettina Keller; Markus Christen; Chris Oostenbrink; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2006-12-16       Impact factor: 2.835

Review 5.  Structural and functional analysis of the Na+/H+ exchanger.

Authors:  Emily R Slepkov; Jan K Rainey; Brian D Sykes; Larry Fliegel
Journal:  Biochem J       Date:  2007-02-01       Impact factor: 3.857

6.  Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G.

Authors:  Jennifer B Hall; David Fushman
Journal:  J Biomol NMR       Date:  2003-11       Impact factor: 2.835

7.  On using time-averaging restraints in molecular dynamics simulation.

Authors:  W R Scott; A E Mark; W F van Gunsteren
Journal:  J Biomol NMR       Date:  1998-11       Impact factor: 2.835

8.  Extensive distance geometry calculations with different NOE calibrations: new criteria for structure selection applied to Sandostatin and BPTI.

Authors:  H Widmer; A Widmer; W Braun
Journal:  J Biomol NMR       Date:  1993-05       Impact factor: 2.835

9.  High-resolution structure and dynamic implications for a double-helical gramicidin A conformer.

Authors:  S M Pascal; T A Cross
Journal:  J Biomol NMR       Date:  1993-09       Impact factor: 2.835

10.  Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.

Authors:  John J Kuszewski; Robin Augustine Thottungal; G Marius Clore; Charles D Schwieters
Journal:  J Biomol NMR       Date:  2008-07-31       Impact factor: 2.835
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