Packing of Side Chains

Offer, G., and Sessions, R. (1995). Computer modelling of the o-helical coiled coil Packing of side-chains in the inner core. J. Mol. Biol. 249, 967-987. 

As O Shea and colleagues (1991) have noted, the packing of side chains at the a and d sites of the GCN4-pl dimer is different. At the d position, the a—(3 bond vector of the side chain points into the interface and directly towards the neighboring helix. This type of geometry, called perpendicular packing by Harbury, precludes, 3-branched residues such as lie and Val from occupying these sites and favors Leu. This is the reason that the leucine zipper is a leucine zipper the hallmark of the bZIP transcription... 

One end of the -barrel is closed by the amino-terminal peptide segment that runs across its bottom between fhe two short loops connecting strands B/C and F/ G, respectively, before it enters into /i-slrarid A. Dense packing of side chains in this region and wifhin the adjacent interior of fhe barrel structure leads to fhe formation of a hydrophobic core. The other end of fhe / -barrel is open to the solvent and forms a characteristic pocket. In the case of RBP, retinol is encapsulated as a ligand and protrudes into the barrel by almost half of its depth. The entrance to the pocket is formed by a set of four loops, which connect fhe eight antiparallel strands in a pairwise fashion. Because of the chalice-like shape of fhe protein (Fig. 8.2) and since many members of fhis family complex lipophilic compounds, the term lipocalins was proposed [25]. 

Figure 19. Schematic diagram of the helix realignment mechanism for gating. The closed state of the channel (top) shows the normal nonparallel alignment of helices that optimizes packing of side chains, shown from the side and from above. The application of a transmembrane potential (bottom indicated by + and —) aligns helix dipoles with the field and increases the diameter of the channel interior due to steric repulsion between monomers.

Fig. 2. Selected architectures of block copolymers (a) diblock (b) triblock (c) comb copolymer consisting of flexible chains (d) rod-coil diblock copolymer consisting of a rodlike block and a coil-like block (e) hairyrods, i.e., comb-block copolymers consisting of rodlike backbone and coil-like side chains and (f) LC coil with a side-chain liquid crystalline (LC) block and a flexible block. Many other variations have been introduced, such as multiblock copolymers, block copolymers consisting of several rodlike blocks, or star-shaped block copolymers. Comb-coil block copolymers with dense packing of side chains are also denoted as molecular bottle brushes, as is illustrated in (g) by a simulated structure of an isolated molecule dissolved in a solvent. (Courtesy of Mika Saariaho.)...

Fig. 2 Unit cells of polymorphs I (a) and I (b) as obtained from molecular dynamics simulations. To highlight the backbone and side chain packing, we use C for crystalline and A for amorphous states, i.e., CA-100 corresponds to a system with a crystalline arrangement of backbones, amorphous packing of side-chains, and regioregularity of 100%. CC-100 corresponds to a system with crystalline side chains and 100% regioregularity. Adapted with permission from PoeUdng et al. [13]. Copyright (2013) American Chemical Society...

If the core structure is accurate enough, the above closure methods generally yield reasonable conformations for short loops (up to six or seven residues) that are relatively well determined by conditions of correct covalent bonding to the rest of the chain, and the correct packing of side chains. By contrast, the conformation of longer loops (n > 7) is heavily affected by nonbonded interactions, as well as solvation and entropic effects. Conformational energy functions without... 

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