Literature DB >> 11061223

On the similarity of properties in solution or in the crystalline state: a molecular dynamics study of hen lysozyme.

U Stocker1, K Spiegel, W F van Gunsteren.   

Abstract

As protein crystals generally possess a high water content, it is assumed that the behaviour of a protein in solution and in crystal environment is very similar. This assumption can be investigated by molecular dynamics (MD) simulation of proteins in the different environments. Two 2ns simulations of hen egg white lysozyme (HEWL) in crystal and solution environment are compared to one another and to experimental data derived from both X-ray and NMR experiments, such as crystallographic B-factors, NOE atom-atom distance bounds, 3J(H N alpha)-coupling constants, and 1H-15N bond vector order parameters. Both MD simulations give very similar results. The crystal simulation reproduces X-ray and NMR data slightly better than the solution simulation.

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Year:  2000        PMID: 11061223     DOI: 10.1023/a:1008379605403

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


  21 in total

1.  Molecular dynamics simulations of human alpha-lactalbumin: changes to the structural and dynamical properties of the protein at low pH.

Authors:  L J Smith; C M Dobson; W F van Gunsteren
Journal:  Proteins       Date:  1999-07-01

2.  Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping.

Authors:  F Yang; C A Bewley; J M Louis; K R Gustafson; M R Boyd; A M Gronenborn; G M Clore; A Wlodawer
Journal:  J Mol Biol       Date:  1999-05-07       Impact factor: 5.469

3.  Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2.

Authors:  W Braun; M Vasák; A H Robbins; C D Stout; G Wagner; J H Kägi; K Wüthrich
Journal:  Proc Natl Acad Sci U S A       Date:  1992-11-01       Impact factor: 11.205

4.  High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin.

Authors:  J M Moore; C A Lepre; G P Gippert; W J Chazin; D A Case; P E Wright
Journal:  J Mol Biol       Date:  1991-09-20       Impact factor: 5.469

5.  Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants.

Authors:  L J Smith; M J Sutcliffe; C Redfield; C M Dobson
Journal:  Biochemistry       Date:  1991-01-29       Impact factor: 3.162

6.  The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure.

Authors:  J Lu; C L Lin; C Tang; J W Ponder; J L Kao; D P Cistola; E Li
Journal:  J Mol Biol       Date:  1999-03-05       Impact factor: 5.469

7.  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

8.  Structure determination and analysis of helix parameters in the DNA decamer d(CATGGCCATG)2 comparison of results from NMR and crystallography.

Authors:  U Dornberger; J Flemming; H Fritzsche
Journal:  J Mol Biol       Date:  1998-12-18       Impact factor: 5.469

9.  Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes.

Authors:  L J Smith; A E Mark; C M Dobson; W F van Gunsteren
Journal:  Biochemistry       Date:  1995-08-29       Impact factor: 3.162

10.  Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure.

Authors:  D Neri; M Billeter; K Wüthrich
Journal:  J Mol Biol       Date:  1992-02-05       Impact factor: 5.469

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  19 in total

1.  Assessing the effect of conformational averaging on the measured values of observables.

Authors:  R Bürgi; J Pitera; W F van Gunsteren
Journal:  J Biomol NMR       Date:  2001-04       Impact factor: 2.835

2.  Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.

Authors:  J W Pitera; M Falta; W F van Gunsteren
Journal:  Biophys J       Date:  2001-06       Impact factor: 4.033

3.  Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.

Authors:  Alexandra Choutko; Alice Glättli; César Fernández; Christian Hilty; Kurt Wüthrich; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2010-10-05       Impact factor: 1.733

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

Authors:  H Schwalbe; S B Grimshaw; A Spencer; M Buck; J Boyd; C M Dobson; C Redfield; L J Smith
Journal:  Protein Sci       Date:  2001-04       Impact factor: 6.725

5.  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

6.  Validation of the 53A6 GROMOS force field.

Authors:  Chris Oostenbrink; Thereza A Soares; Nico F A van der Vegt; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2005-04-01       Impact factor: 1.733

7.  Cold-active enzymes studied by comparative molecular dynamics simulation.

Authors:  Vojtech Spiwok; Petra Lipovová; Tereza Skálová; Jarmila Dusková; Jan Dohnálek; Jindrich Hasek; Nicholas J Russell; Blanka Králová
Journal:  J Mol Model       Date:  2007-01-18       Impact factor: 1.810

8.  Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

Authors:  Pawel A Janowski; Chunmei Liu; Jason Deckman; David A Case
Journal:  Protein Sci       Date:  2015-06-11       Impact factor: 6.725

Review 9.  X-ray Scattering Studies of Protein Structural Dynamics.

Authors:  Steve P Meisburger; William C Thomas; Maxwell B Watkins; Nozomi Ando
Journal:  Chem Rev       Date:  2017-05-30       Impact factor: 60.622

10.  Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.

Authors:  Yi Xue; Nikolai R Skrynnikov
Journal:  Protein Sci       Date:  2014-04       Impact factor: 6.725

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