Backbone-side chain interactions

Newman diagrams for protein backbone-side-chain interactions. (A) Backbone-independent interactions, looking down the Ca-C/f bond from Cfl certain combinations of X and Xi are forbidden because of close interactions between C<5 and backbone N and C of the same residue. In the lower diagram, the X2 = 180° rotamer is pointing towards the viewer. The four i, 2 combinations which... 

Keywords Amide Amino-acid Backbone-side chain interactions Conformation-selective IR spectroscopy Gas phase laser spectroscopy Hydrates Secondary structures Supersonic expansion... 

Other backbone-side chain interactions have been documented for specific residues. A C6 H-bond linking the S atom of methionine to its NHbb group has been observed in model capped dipeptides [109], mimicking a folding pattern also... 

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. 

Figure 1. A two-dimensional representation that illustrates the tracing of the interaction lines to give the peak-pass-peak-pass chain representative of the protein backbone, side chains and disulphide bridge. Circles represent passes and squares peaks. 

The first approach has successfully been applied to the study of amorphous as well as to macroscopically ordered solids. Examples of applications include the determination of backbone geometries in fibrous proteins [4] or the determination of protein-backbone, side-chain, and bound-ligand orientation with respect to the membrane normal in membrane-bound proteins [5-8]. Membranes, bilayers, bicelles, or liposomes are neither solid nor liquid systems but have aspects of both and are sometimes liquid crystalline. In most of these systems, time-independent anisotropic interactions play an important role,... 

Gly is another helix breaker and is often found at the C-terminus of a helix. The lack of a side chain in the a-carbon of Gly not only deprives it of helix-promoting side-chain interactions, but also increases its backbone conformational flexibility, favoring a random coil conformation. 

A large number of chemical and physical properties, manifest in the amino acid side chains, have been thoroughly examined by many investigators. Attempts have been made to correlate these properties with their relatedness among protein sequences. What is most relevant is how these side chains interact with the backbone and with one another and what roles they each play within particular types of secondary and tertiary structure. The parametric description of residue environments with the help of solvent accessibility, secondary structure, backbone torsion angles, pairwise residue-residue distances, or Ca positions is the comparison between amino acid types at protein sequence positions and residue locations in structural templates. A recent review has evaluated and quantified the extent to which the amino acid type-specific distributions of commonly used environment parameters discriminate with respect to the 20 amino acid types (Sunyaev et al., 1998). Some of the important amino acid properties and residue environments are discussed below. 

The introduction of conformational constraints should influence the backbone conformation without compromising any crucial side chain interaction with the receptor. 

The authors studied the interaction of CDs with alkyl side chains attached to the poly(acrylamide) backbone with NMR spectroscopy and found that CDs bind alkyl side chains efficiently and selectively [156]. n-Butyl side chains interacted only with a-CD. On the other hand, t-butyl side chains interacted with j6-CD and y-CD, but did not interact with a-CD. The association constant for the complex formation of fi-CD with a t-butyl side chain was larger than that for the complex formation of y-CD, indicating that the t-butyl side chain fits well in the /3-CD cavity. The association constant for the complex formation of a-CD with linear alkyl side chains increased with an increase in the carbon number of the alkyl side chain from butyl to dodecyl. Noteworthy is that CDs recognize alkyl chains on the polymer main chain more specifically than low molecular weight ones. This may be because CDs include polymer-carrying alkyl chains only from one direction. 

The crystal structure of a very short patch repair (Vsr) endonuclease complex with DNA containing a TG mismatch shows novel interactions of intercalated aromatic side chains which recognise the mismatch site. The enzyme also distorts the DNA backbone, and many protein side chain interactions stabilise the complex. Crystallographic studies of duplexes containing the mutagenic... 

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