Literature DB >> 11274458

A refined solution structure of hen lysozyme determined using residual dipolar coupling data.

H Schwalbe1, S B Grimshaw, A Spencer, M Buck, J Boyd, C M Dobson, C Redfield, L J Smith.   

Abstract

A high resolution NMR structure of hen lysozyme has been determined using 209 residual 1H-15N dipolar coupling restraints from measurements made in two different dilute liquid crystalline phases (bicelles) in conjunction with a data set of 1632 NOE distance restraints, 110 torsion angle restraints, and 60 hydrogen bond restraints. The ensemble of 50 low-energy calculated structures has an average backbone RMSD of 0.50+/-0.13A to the mean structure and of 1.49+/-0.10A to the crystal structure of hen lysozyme. To assess the importance of the dipolar coupling data in the structure determination, the final structures are compared with an ensemble calculated using an identical protocol but excluding the dipolar coupling restraints. The comparison shows that structures calculated with the dipolar coupling data are more similar to the crystal structure than those calculated without, and have better stereochemical quality. The structures also show improved quality factors when compared with additional dipolar coupling data that were not included in the structure calculations, with orientation-dependent 15N chemical shift changes measured in the bicelle solutions, and with T1/T2 values obtained from 15N relaxation measurements. Analysis of the ensemble of NMR structures and comparisons with crystal structures, 15N relaxation data, and molecular dynamics simulations of hen lysozyme provides a detailed description of the solution structure of this protein and insights into its dynamical behavior.

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Year:  2001        PMID: 11274458      PMCID: PMC2373969          DOI: 10.1110/ps.43301

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  37 in total

1.  Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases.

Authors:  M A Markus; R B Gerstner; D E Draper; D A Torchia
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  Assessment of zinc finger orientations by residual dipolar coupling constants.

Authors:  V Tsui; L Zhu; T H Huang; P E Wright; D A Case
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

3.  Integration of spin-state-selective excitation into 2D NMR correlation experiments with the heteronuclear ZQ/2Q pi rotations for 1JXH- resolved E.COSY-type measurements of heteronuclear coupling constants in proteins.

Authors:  A Meissner; J O Duus; O W Sørensen
Journal:  J Biomol NMR       Date:  1997-07       Impact factor: 2.835

4.  Determination of a complete set of coupling constants in 13C-labeled oligonucleotides.

Authors:  H Schwalbe; J P Marino; G C King; R Wechselberger; W Bermel; C Griesinger
Journal:  J Biomol NMR       Date:  1994-09       Impact factor: 2.835

Review 5.  Understanding how proteins fold: the lysozyme story so far.

Authors:  C M Dobson; P A Evans; S E Radford
Journal:  Trends Biochem Sci       Date:  1994-01       Impact factor: 13.807

Review 6.  What's new in lysozyme research? Always a model system, today as yesterday.

Authors:  P Jollès; J Jollès
Journal:  Mol Cell Biochem       Date:  1984-09       Impact factor: 3.396

7.  Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.

Authors:  K Wüthrich; M Billeter; W Braun
Journal:  J Mol Biol       Date:  1983-10-05       Impact factor: 5.469

8.  Efficient production from Aspergillus niger of a heterologous protein and an individual protein domain, heavy isotope-labelled, for structure-function analysis.

Authors:  D A MacKenzie; J A Spencer; M F Le Gal-Coëffet; D B Archer
Journal:  J Biotechnol       Date:  1996-04-30       Impact factor: 3.307

9.  Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.

Authors:  M Buck; J Boyd; C Redfield; D A MacKenzie; D J Jeenes; D B Archer; C M Dobson
Journal:  Biochemistry       Date:  1995-03-28       Impact factor: 3.162

10.  Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules.

Authors:  M Ottiger; A Bax
Journal:  J Biomol NMR       Date:  1998-10       Impact factor: 2.835

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  58 in total

1.  Structure refinement of flexible proteins using dipolar couplings: application to the protein p8MTCP1.

Authors:  Hélène Déméné; Thierry Ducat; Philippe Barthe; Marc-André Delsuc; Christian Roumestand
Journal:  J Biomol NMR       Date:  2002-01       Impact factor: 2.835

2.  Protein structure prediction using sparse dipolar coupling data.

Authors:  Youxing Qu; Jun-tao Guo; Victor Olman; Ying Xu
Journal:  Nucleic Acids Res       Date:  2004-01-26       Impact factor: 16.971

3.  Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.

Authors:  Deyou Zheng; James M Aramini; Gaetano T Montelione
Journal:  Protein Sci       Date:  2004-01-10       Impact factor: 6.725

4.  On the evaluation and optimization of protein X-ray structures for pKa calculations.

Authors:  Jens Erik Nielsen; J Andrew McCammon
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

5.  Residue-specific α-helix propensities from molecular simulation.

Authors:  Robert B Best; David de Sancho; Jeetain Mittal
Journal:  Biophys J       Date:  2012-03-20       Impact factor: 4.033

6.  Molecular dynamics simulation of thionated hen egg white lysozyme.

Authors:  Wei Huang; Andreas P Eichenberger; Wilfred F van Gunsteren
Journal:  Protein Sci       Date:  2012-06-25       Impact factor: 6.725

7.  On the calculation of ³Jαβ-coupling constants for side chains in proteins.

Authors:  Denise Steiner; Jane R Allison; Andreas P Eichenberger; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2012-06-20       Impact factor: 2.835

8.  Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics.

Authors:  Filip Meersman; Canan Atilgan; Andrew J Miles; Reto Bader; Weifeng Shang; André Matagne; B A Wallace; Michel H J Koch
Journal:  Biophys J       Date:  2010-10-06       Impact factor: 4.033

9.  Residual dipolar couplings: are multiple independent alignments always possible?

Authors:  Victoria A Higman; Jonathan Boyd; Lorna J Smith; Christina Redfield
Journal:  J Biomol NMR       Date:  2010-12-24       Impact factor: 2.835

10.  Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

Authors:  T A Soares; X Daura; C Oostenbrink; L J Smith; W F van Gunsteren
Journal:  J Biomol NMR       Date:  2004-12       Impact factor: 2.835

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