Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace

R.M. Scheek; N.A.J. van Nuland; B.L. de Groot; A Amadei

doi:10.1007/bf00417496

Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace

R.M. Scheek^*
, N.A.J. van Nuland
, B.L. de Groot
, A Amadei

^*Corresponding author for this work

Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

20 Citations (Scopus)

Abstract

We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem.

Original language	English
Pages (from-to)	106-111
Number of pages	6
Journal	Journal of Biomolecular Nmr
Volume	6
Issue number	1
DOIs	https://doi.org/10.1007/bf00417496
Publication status	Published - Jul-1995

Keywords

MOLECULAR DYNAMICS
ESSENTIAL DYNAMICS
PROTEIN STRUCTURE
DISTANCE RESTRAINTS
NUCLEAR-MAGNETIC-RESONANCE
PROTEINS
GEOMETRY

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Structure from NMR and molecular dynamics Distance restraining
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title = "Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace",

abstract = "We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem.",

keywords = "MOLECULAR DYNAMICS, ESSENTIAL DYNAMICS, PROTEIN STRUCTURE, DISTANCE RESTRAINTS, NUCLEAR-MAGNETIC-RESONANCE, PROTEINS, GEOMETRY",

author = "R.M. Scheek and \{van Nuland\}, N.A.J. and \{de Groot\}, B.L. and A Amadei",

note = "Journal UL P505 BIOMOL NMR",

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pages = "106--111",

journal = "Journal of Biomolecular Nmr",

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T1 - Structure from NMR and molecular dynamics

T2 - Distance restraining inhibits motion in the essential subspace

AU - Scheek, R.M.

AU - van Nuland, N.A.J.

AU - de Groot, B.L.

AU - Amadei, A

N1 - Journal UL P505 BIOMOL NMR

PY - 1995/7

Y1 - 1995/7

N2 - We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem.

AB - We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem.

KW - MOLECULAR DYNAMICS

KW - ESSENTIAL DYNAMICS

KW - PROTEIN STRUCTURE

KW - DISTANCE RESTRAINTS

KW - NUCLEAR-MAGNETIC-RESONANCE

KW - PROTEINS

KW - GEOMETRY

U2 - 10.1007/bf00417496

DO - 10.1007/bf00417496

M3 - Comment/Letter to the editor

SN - 0925-2738

VL - 6

SP - 106

EP - 111

JO - Journal of Biomolecular Nmr

JF - Journal of Biomolecular Nmr

IS - 1

ER -

Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace

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Keywords

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