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Seth Blumenthal , Lehigh University, Bethlehem
Yisheng Tang , Lehigh University, Bethlehem
Wenjie Yang , Lehigh University, Bethlehem
Brian Chen , Lehigh University, Bethlehem
ABSTRACT
Electrostatic focusing is a general phenomenon that occurs in cavities and grooves on the molecular surface of biomolecules. Narrow surface features can partially shield charged atoms from the high dielectric solvent, enhancing electrostatic potentials inside the cavity and projecting electric field lines outwards into the solvent. This effect has been observed in many instances and is widely considered in the human examination of molecular structure, but it is rarely integrated into the digital representations used in protein structure comparison software. To create a computational representation of electrostatic focusing that is compatible with structure comparison algorithms, this paper presents an approach that generates three dimensional solids that approximate regions where focusing occurs. We verify the accuracy of this representation against instances of focusing in proteins and DNA. Noting that this representation also identifies thin focusing regions on the molecular surface that are unlikely to affect binding, we describe a second algorithm that conservatively isolates larger focusing regions. The resulting three dimensional solids can be compared with Boolean Set operations, permitting a new range of analyses on the regions where electrostatic focusing occurs. They also represent a novel integration of molecular shape and electrostatic focusing into the same structure comparison framework.
INDEX TERMS
Biology and genetics, Curve, surface, solid, and object representations, Chemistry
CITATION
Seth Blumenthal, Yisheng Tang, Wenjie Yang, Brian Chen, "Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure", IEEE/ACM Transactions on Computational Biology and Bioinformatics, , no. 1, pp. 1, PrePrints PrePrints, doi:10.1109/TCBB.2013.124
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