An extended sampling of the configurational space of HPr from E. coli

Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615–626; de Groot et al., J. Biomol. Str. Dyn. 13: 741–751, 1996) to obtain an extended sampling of the configurational space of proteins, using an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al., Proteins 17:412–425, 1993) method. In the present study, this ED sampling technique is applied to the histidine‐containing phosphocarrier protein HPr from Escherichia coli. We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. The structures in this cluster are geometrically and energetically comparable to NMR structures. Moreover, on average, this large cluster satisfies nearly all NMR‐derived distance restraints. © 1996 Wiley‐Liss, Inc.

[1]  H J Berendsen,et al.  Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. , 1996, Journal of biomolecular structure & dynamics.

[2]  B. L. de Groot,et al.  Phosphorylation‐induced torsion‐angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement , 1996, Protein science : a publication of the Protein Society.

[3]  K. Schulten,et al.  Principal Component Analysis and Long Time Protein Dynamics , 1996 .

[4]  H J Berendsen,et al.  An efficient method for sampling the essential subspace of proteins. , 1996, Journal of biomolecular structure & dynamics.

[5]  C. Sander,et al.  A comparison of structural and dynamic properties of different simulation methods applied to SH3. , 1996, Biophysical journal.

[6]  Dusanka Janezic,et al.  Harmonic analysis of large systems. III. Comparison with molecular dynamics , 1995, J. Comput. Chem..

[7]  H. Berendsen,et al.  Essential dynamics of the cellular retinol-binding protein--evidence for ligand-induced conformational changes. , 1995, Protein engineering.

[8]  A. Amadei,et al.  Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace , 1995, Journal of biomolecular NMR.

[9]  B M Pettitt,et al.  A sampling problem in molecular dynamics simulations of macromolecules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  G. Robillard,et al.  High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data. , 1995, Journal of molecular biology.

[11]  G. Robillard,et al.  THE HIGH-RESOLUTION STRUCTURE OF THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI DETERMINED BY RESTRAINED MOLECULAR DYNAMICS FROM NMR NUCLEAR OVERHAUSER EFFECT DATA , 1994 .

[12]  H. Berendsen,et al.  The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data. , 1994, Journal of molecular biology.

[13]  L. Delbaere,et al.  The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. , 1994, The Journal of biological chemistry.

[14]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[15]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[16]  L. Delbaere,et al.  Active-centre torsion-angle strain revealed in 1.6 Å-resolution structure of histidine-containing phosphocarrier protein , 1993, Nature.

[17]  G R Jacobson,et al.  Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. , 1993, Microbiological reviews.

[18]  García,et al.  Large-amplitude nonlinear motions in proteins. , 1992, Physical review letters.

[19]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[20]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[21]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.