| DOI: 10.1093/nar/gkg162 Small worlds in RNA structures (2002) | |||||||||||||||
Abstract | |||||||||||||||
| I consider conformational spaces of tRNAphe de®ned by sets of suboptimal structures from the perspective of small-world networks. Herein, the in¯uence of modi®cations on typical small-world network properties and the shape of energy landscapes is discussed. Results indicate that natural modi®cations in¯uence the degree of local clustering and mean path lengths far more than random or no modi®cations. High frequencies in the thermodynamic ensemble coincide with high numbers of neighboring structures that one conformation can adopt by one elementary move. Conformation spaces indicate the existence of modular substructures. It can be shown that modi®cations leave the nature of small-world topology untouched albeit natural modi®cations have a reasonable enhancing and streamlining effect on the degree of clustering and therefore on the substructures of the conformational space. | |||||||||||||||
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