Letter | Published:

Collective variable description of small-amplitude conformational fluctuations in a globular protein

Nature volume 296, pages 776778 (22 April 1982) | Download Citation

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Abstract

Globular proteins in the native state undergo small-amplitude conformational fluctuations1, which can be observed experimentally, for example, as temperature factors in X-ray crystallography2–5 or through their effects on the relaxation times in NMR6. The fluctuations can also be observed as the trajectories of each atom of a protein molecule generated by the theoretical method of molecular dynamics5,7,8. These studies indicate that atoms or groups of atoms in the molecule, especially those near the surface, are in a ‘fluid-like’ state, which means that the forces acting on them have an impulsive character and the temperature factors obtained from X-ray crystallography have an anharmonic temperature dependence. More work is clearly needed to characterize better the state of the protein interior. Thus we have now calculated the shape of the conformational energy surface of a small protein, basic pancreatic trypsin inhibitor (BPTI), near its minimum. We find that for most degrees of freedom corresponding to collective conformational changes, the protein molecule behaves harmonically or like a solid.

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Affiliations

  1. Department of Physics, Faculty of Science, Kyushu University 33, Fukuoka 812, Japan

    • Tosiyuki Noguti
    •  & Nobuhiro Gō

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DOI

https://doi.org/10.1038/296776a0

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