Interactions side chain

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

Figure 10.18 Side-chain interactions in the leucine zipper structure, (a) The hydrophobic side chains in spikes a and d (see Figure 10.17) form a hydrophobic core between the two coiled a helices, (b) Charged side chains in spikes and g can promote dimer formation by forming complementary charge interactions between the two a helices.

Long side chain Interaction in long side chain Flexible backbone... 

In the bilayer or upon interaction with detergent micelles, a structural reorganization of pardaxin aggregates takes place, in which the polar side chains interact with themselves and the hydrophobic residues are externally oriented in the pardaxin aggregate, therefore allowing interactions with the lipid backbone hydrocarbons. 

Shoemaker KR, Fairman R, Schultz DA, Robertson AD, York EJ, Stewart JM, Baldwin RL (1990) Side-chain interactions in the C-peptide helix Phe8-Hisl2+. Biopolymers 29 1-11. 

Although additional experiments and simulations are needed to determine how much of reality is captured in this model, it does explain one important property of proteins their rapid rate of refolding, which is independent of denaturation conditions. If the polypeptide chain is unable to escape from this steric trap and access conformations with the wrong topology, it could never wander far from the folded conformation and thereby avoid incorrect side chain/side chain interactions. 

Sodium hyaluronate crystallizes in a hexagonal unit-cell with a = 11.7 A (1.17 nm) and c = 28.5 A (2.85 nm). Another form, produced by annealing, packs in a hexagonal unit-cell with a = 18.7 A (1.87 nm) and c = 28.5 A (2.85 nm). The conformation of the chain is a threefold helix. The significance of the side-chain interaction was discussed, and different packing schemes were proposed for the two types of unit cell. 

Singh, J. and Thornton, J. M. (1992). Atlas of Protein Side-Chain Interactions, Vols. 1 and 2. IRL Press, Oxford, UK. 

Bond, J. P., Deverin, S. P., Inouye, H., el-Agnaf, O. M., Teeter, M. M., and Kirschner, D. A. (2003). Assemblies of Alzheimer s peptides A beta 25—35 and A beta 31-35 Reverse-turn conformation and side-chain interactions revealed by X-ray diffraction./. Struct. Biol. 141, 156-170. 

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