Geometry packing motifs

Determination of the crystal structures to obtain the geometrical information— molecular geometries and packing motif—of the various polymorphs. 

Fig. 4.18 Some of the various hybrid geometries and packing motifs possible upon molecule grafting to the surface of a spherical nanoparticle. The role of the molecules in migrating and deforming at the surface was crucial in providing these structures [129]. Copyright from Beilstein Journal of Organic Chemistry 2012...

The crystal structure of the N-terminal 80 residues of tropomyosin (Brown et al., 2001) contains its first alanine cluster and displays two specific consequences of this motif for the main-chain geometry of the coiled-coil. One is that the coiled-coil in this segment becomes locally narrow, to 8.0 A diameter, as would be expected from alanine s small size. This feature is directly related to the stability of the coiled-coil in a 10 A wide dimeric coiled-coil, a pair of core alanines from the opposite helices would generally leave unfilled spaces in the interior these spaces become smaller as the main chains of the helices approach each other and the core becomes more close-packed. Recent studies of model coiled-coils with identical amino acid compositions, but different arrangements,... 

Due to the small number of secondary-structural types found in proteins, only a limited number of simple supersecondary-structural motifs such as aa, PP, PaP,..., are possible. Moreover, as discussed by Chothia and co-workers in a number of papers [23,24], the packing geometries available to each supersecondary-structural motif are also quite limited specifically, the relative orientations of two a-helices, of an a-helix and a P-sheet, and of two P-sheets exhibit limited distributions. These disuibutions have been interpreted both in geometric terms, based on the surface topography of the interacting secondary-structural elements [20,23-26], and in energetic terms, based on the molecular mechanics calculations of Chou et al [27]. 

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