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Fractal Dimensions of Macromolecular Structures.

  • Todoroff N Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland fax: (+41) 44 633 13 79.
  • Kunze J Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland fax: (+41) 44 633 13 79.
  • Schreuder H Sanofi-Aventis Deutschland GmbH R&D Frankfurt am Main, Germany.
  • Hessler G Sanofi-Aventis Deutschland GmbH R&D Frankfurt am Main, Germany.
  • Baringhaus KH Sanofi-Aventis Deutschland GmbH R&D Frankfurt am Main, Germany.
  • Schneider G Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland fax: (+41) 44 633 13 79.
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  • 2015-07-28
Published in:
  • Molecular informatics. - 2014
Computational chemistry
Drug discovery
Fractal
Ligand binding
Protein structure
English Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less-explored geometric features of macromolecules is molecular surface irregularity, or 'roughness', which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified the surface roughnesses of biological macromolecules in a large-scale survey that revealed D values between 2.0 and 2.4. The results of our study imply that surface patches involved in molecular interactions, such as ligand-binding pockets and protein-protein interfaces, exhibit greater local fluctuations in their fractal dimensions than 'inert' surface areas. We expect approximately 22 % of a protein's surface outside of the crystallographically known ligand binding sites to be ligandable. These findings provide a fresh perspective on macromolecular structure and have considerable implications for drug design as well as chemical and systems biology.
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  • English
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green
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https://sonar.ch/global/documents/153602
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