Treatment of small deformations of polyhedral shapes of functional group distributions in biomolecules

✍ Scribed by Paul G. Mezey; Kenichi Fukui; Shigeru Arimoto

• Publisher: John Wiley and Sons
• Year: 2000
• Tongue: English
• Weight: 395 KB
• Volume: 76
• Category: Article
• ISSN: 0020-7608
• DOI: 10.1002/(sici)1097-461x(2000)76:6<756::aid-qua8>3.0.co;2-u

✦ Synopsis

Polyhedral models of the distribution of the essential functional groups (the EFG polyhedra) within biomolecules provide simple tools for the study of small deformations affecting the mutual positioning of functional groups. In general, the relative locations of various functional groups may have an important role in determining the biochemical activities of biomolecules; the mere presence of functional groups is often insufficient to ensure a given biochemical effect linked to the functional group. Accessibility and the possibility of geometrically constrained, concerted action of several functional groups are of major importance in many instances. Often, small molecular deformations have a crucial role. In order to describe small deformations of biomolecules, two polyhedral deformation approaches are implemented for the entire electron density. The repositioning of essential functional groups generates a typically nonlinear deformation of the electron density that can be modeled by a nonlinear deformation of the entire three-dimensional space. These nonlinear deformations reproduce exactly the new locations of the reference points of the essential functional groups, and approximate the electron density of the new EFG polyhedron using either of two simple algorithms, the dimension expansion-reduction (DER) or the weighted affine transformation (WAT) algorithm. The adaptation of these two techniques to deformations defined in terms of the large scale EFG features of biomolecules is described.