Simultaneous determination of protein structure and dynamics

TY - JOUR

T1 - Simultaneous determination of protein structure and dynamics

AU - Lindorff-Larsen, Kresten

AU - Best, Robert B.

AU - DePristo, M. A.

AU - Dobson, C. M.

AU - Vendruscolo, Michele

PY - 2005

Y1 - 2005

N2 - We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.

AB - We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.

U2 - 10.1038/nature03199

DO - 10.1038/nature03199

M3 - Journal article

C2 - 15650731

SN - 0028-0836

VL - 433

SP - 128

EP - 132

JO - Nature

JF - Nature

IS - 7022

ER -