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

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 crystallography^2–5 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 dynamics^5,7,8. 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.