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The Gaussian network model (GNM) is a representation of a biological macromolecule as an elastic mass-and-spring network to study, understand, and characterize mechanical aspects of its long-scale dynamics. The model has a wide range of applications from small proteins such as enzymes composed of a single domain, to large macromolecular assemblies such as a ribosome or a viral capsid. Protein domain dynamics plays key roles in a multitude of molecular recognition and cell signalling processes. Protein domains, connected by intrinsically disordered flexible linker domains, induce long-range allostery via protein domain dynamics. The resultant dynamic modes cannot be generally predicted from static structures of either the entire protein or individual domains. The Gaussian network model is a minimalist, coarse-grained approach to study biological molecules. In the model, proteins are represented by nodes corresponding to alpha carbons of the amino acid residues. Similarly, DNA and RNA structures are represented with one to three nodes for each nucleotide. The model uses the harmonic approximation to model interactions, i.e. the spatial interactions between nodes (amino acids or nucleotides) are modeled with a uniform harmonic spring. This coarse-grained representation makes the calculations computationally inexpensive. At molecular level, many biological phenomena, such as catalytic activity of an enzyme, occur within the range of nano- to millisecond timescales. All atom simulation techniques, such as molecular dynamics, rarely reach microsecond trajectory length, depending on the size of the system and accessible computational resources. Normal mode analysis in the context of GNM or elastic network (EN) models, in general, provides insights on the longer-scale functional behaviors of macromolecules. Here, the model captures native state functional motions of a biomolecule in the cost of atomic detail. The inference obtained from this model is complementary to atomic detail simulation techniques. Another model for protein dynamics based on elastic mass-and-spring networks is the Anisotropic Network Model. == Gaussian network model theory == The Gaussian network model was first proposed in 1996 by Tirion at the atomic level〔Tirion, M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett., 77, 1905, 1996.〕 and then one year later reconsidered at the amino-acid level by Bahar, Atilgan, Haliloglu and Erman.〔Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential, I. Bahar, A. R. Atilgan, and B. Erman Folding & Design 2, 173-181, 1997.〕〔Gaussian dynamics of folded proteins, Haliloglu, T. Bahar, I. & Erman, B. Phys. Rev. Lett. 79, 3090-3093, 1997.〕 The model was influenced by work of PJ Flory on polymer networks 〔Flory, P.J., Statistical thermodynamics of random networks, Proc. Roy. Soc. Lond. A, 351, 351, 1976.〕 and other works that utilized normal mode analysis and simplified harmonic potentials to study dynamics of proteins.〔Go, N., Noguti, T. and Nishikawa, T. Dynamics of a small globular protein in terms of low-frequency vibrational modes, Proc. Natl. Acad. Sci. USA, 80, 3696, 1983.〕 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Gaussian network model」の詳細全文を読む スポンサード リンク
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