Side-chain packing

SY Chung, S Subbiah. The use of side-chain packing methods m modeling bacteriophage repressor and cro proteins. Pi-otem Sci 4 2300-2309, 1995. 

Figure 3.8 Schematic diagram of the dimeric Rop molecule. Each subunit comprises two a helices arranged in a coiled-coil structure with side chains packed into the hydrophobic core according to the "knobs in holes" model. The two subunits are arranged in such a way that a bundle of four a helices is formed.

The membrane is a dynamic assembly and things are diffusing rapidly in the plane of the bilayer. The middle of the bilayer has been likened to olive oil. As with oil, cooling the lipid bilayer will cause the hydrocarbons to become more ordered (structured). The side chains pack closer to each other, and the fluidity of the membrane is lower. Things that disrupt the ability of the side chains to pack in a regular fashion make the membrane more fluid (Fig. 3-4). These include high temperature, lipids with shorter chains (double bonds. The shorter lipids and the m-double bonds cause the occurrence of holes (packing defects). 

Marsh et al, 1955a,b), shows that the side chains pack closely against one other. 

Contrasting with these, the CH3-terminated 99 did show a Cotton effect. This is because the chiral side chain is / -branched, so that the chiral locking effect is sufficient to afford a stable PSS conformation. CF3-terminated 98 also showed a Cotton effect, though the CD and also UV intensity were about half those of 99, presumably due to some competition between the C-F- -Si interaction and chiral side-chain packing effects. 

The ways in which a-helices pack against one another were initially described by Crick (1953) as knobs into holes side chain packing which could work at either a shallow left-handed crossing angle or a... 

Petersen et al., Petersen and Voth,i Spohr, Spohr et al., and Walbran and Kornyshev developed EVB-based models to study the effect of con-finemenf in nanometer-sized pores and fhe role of acid-functionalized polymer walls on solvation and transport of protons in PEMs. The calculations by the Voth group revealed an inhibiting effect of sulfonate ions on proton motions. The EVB model by Kornyshev, Spohr, and Walbran was specifically designed to sfudy effecfs on proton mobilify due to charge delocalization within SOg groups, side chain packing density, and fluctuations... 

The high thermostability in the thermophilic counterpart was due to amino acid residues located in three distal regions of the protein as shown in Fig. 2. " The introduction of five selected mutations in those regions of Pac-55 caused the protein to attain a similar thermostability to that of the thermophilic protein probably due to a tighter side chain packing and increased total accessible surface area. " ... 

It is interesting that although the Val-143— His mutation leads to a bulky side chain at the base of the hydrophobic pocket, the mutant enzyme exhibits only a 10 -fold loss of CO2 hydrase activity relative to the wild-type enzyme (Fierke et ai, 1991). In this mutant the Val-I43- His side chain packs differently in the pocket relative to the side chains of the Val-143—>Phe and Val-143- Tyr mutants (Alexander et ai, 1991). It is likely that differences in side-chain packing, as well as differences involving active-site solvent structure, are responsible for differences in enzyme-substrate association behavior among the residue-143 mutants of carbonic anhydrase II. 

Sickle cell disease 16, 359, 360 Side chains packing 75 Siderophilins 840 Siderophore(s) 838, 838s chelate effect 310 receptors 839 Sieve plates 30 Signal peptidase 522, 620 Signal recognition particle (SRP) 520 Signal sequences 519 Signaling 1... 

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