Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables |
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| Institution: | 1. School of Social Sciences, Waseda University, Shinjuku, Tokyo 169-8050, Japan;2. Department of Physics, Faculty of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan;3. Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada;5. Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada;4. Department of Biomedical Science and Technology, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy;1. Institut für Neurophysiologie, Medizinische Hochschule Hannover, Hannover, Germany;1. Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China;2. Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China;3. Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;4. Department of Biology, Duke University, 124 Science Drive, Box 90388, Durham, NC 27708, USA |
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| Abstract: | We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system. |
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| Keywords: | Elastic network model Normal mode analysis Dihedral angle space Protein Data Bank Protein–DNA complex Protein–tRNA complex |
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