ABSTRACT
CONTENTS 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 4.2 Basic Theories and Implementations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
4.2.1 NMAwith Hybrid QM/MM Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . 67 4.2.2 Coarse-Grained NMAwith Physical Potentials . . . . . . . . . . . . . . . . . 69
4.3 Illustrative Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 4.3.1 Active Site of Mb-CO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 4.3.2 Flexibility of Molecular Machines — Comparison between
BNM and ANM .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 4.3.2.1 The Hammerhead Ribozyme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 4.3.2.2 The 30S and 50S Ribosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.4 Conclusions and Future Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Normal mode analysis (NMA), a simple but powerful approach, finds its value in many research areas including chemistry [1], structural biology [2], and solid-state physics [3, 4]. The basic information available from NMA includes the frequency and direction of motions, which makes NMA valuable in the interpretation (assignment) of experimental data [5] such as spectra and scattering profiles that encode structural and dynamical information.
