ISSN:
0192-8651
Keywords:
Voronoi volumes
;
packing of atoms
;
density
;
proteins
;
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
In computing the volume occupied by atoms and the density in proteins, one is faced with the problem of intersecting spheres. To estimate either, the space between the atoms has to be divided according to the location of the atoms relative to each other. Various methods, based on Voronoi's idea of approximating the atomic space by polyhedra, have been proposed for this purpose. Comparing procedures concerned with the allocation of space among distinct atoms, we observe different partitionings of space, with deviations of more than 100% for particular atoms. Furthermore, we find that the separating planes of different Voronoi procedures do not meet the intersection circles of covalently linked atoms. This leads to a misallocation of space of up to 7% for atom pairs that largely differ in atomic size (e.g., C - H). Several algorithms are negatively affected by small unallocated polyhedra (“vertex error”). These effects are cumulative for a small protein up to a loss of some 60 Å3 of total volume, which would correspond to the deletion of one complete residue. To overcome these errors, instead of using dividing planes between the atoms, we use curved surfaces, defined as the set of those geometrical loci with equal orthogonal distance to the surfaces of the van der Waals spheres under consideration. The proposed dividing surface meets not only the intersection circle of the two van der Waals spheres but also the intersection circle of the two spheres enlarged by an arbitrary value (e.g., radius of water). This hyperbolic surface enveloping the Voronoi cell can be easily constructed and offers the following advantages: no misallocation of volume for atoms of different size, no vertex error, geometrically reasonable allocation of the volume among atoms, avoidance of discontinuities between neighboring atoms, and improved applicability to water-accessible protein surfaces. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1113-1123
Additional Material:
3 Ill.
Type of Medium:
Electronic Resource
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