A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis.
An exact theorem is proved and its implication is discussed. The theorem states that, if a large molecule, typically biological macromolecules such as proteins, undergoes small-amplitude conformational fluctuations around its native conformation in such a way that within the range of conformational fluctuations at thermal equilibrium the conformational energy surface can be approximated by a multidimensional parabola, then the mass-weighted mean-square displacement of constituent atoms is given by the sum of the contributions from each normal mode of conformational vibration, which in turn is proportional to the inverse of the square of its frequency. This theorem provides a firm theoretical basis for the fact hitherto empirically recognized in the conformational dynamics of, for instance, native proteins that very-low-frequency normal modes make dominant contributions to the conformational fluctuations at thermal equilibrium. Discussion is given on the implication of this theorem, especially on the importance of the concept of the low-frequency normal modes, even in the case where the basic assumption of the harmonicity of the energy surface does not hold.
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Department of Chemistry, Faculty of Science, Kyoto University, Japan.
D004247:DNA; D008433:Mathematics; D008962:Models, Theoretical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
D004247:DNA