Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of deca‐alanine

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Abstract
Effects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α‐helix of deca‐alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one‐to‐one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm−1 and those in the DAS with frequencies less than 164 cm−1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very‐low‐frequency normal modes in the CCS with frequencies less than 128 cm−1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low‐frequency motions are concerned. Based on the results of calculation, mechanical property of the α‐helix of deca‐alanine is discussed.

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