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2014 ; 33
(9
): 588-596
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Fractal Dimensions of Macromolecular Structures
#MMPMID26213587
Todoroff N
; Kunze J
; Schreuder H
; Hessler G
; Baringhaus KH
; Schneider G
Mol Inform
2014[Sep]; 33
(9
): 588-596
PMID26213587
show ga
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.