Coiled coil structures structural diversity

The complexity and diversity of structures in the native proteins eluded any attempt to produce some simple conformation that accounted for their interfacial properties. The study of synthetic polypeptides with non-polar side chains has provided good evidence to support the view that the a-helix can be stable at the air-water interface (5), and it is therefore possible that the interfacial denaturation of proteins is mainly a loss of the tertiary structure (6, 7, 8). Since for a typical protein an a-helix takes up about the same area per residue as the p conformation, it can be accommodated as easily. Moreover, like the p conformation but unlike a more randomly coiled structure, it is linear and therefore compatible with a plane surface without loss of configurational entropy (5). In this respect a plane surface may favor an ordered over a more random structure. The loss of solubility of the spread protein can then be attributed to intermolecular association between hydrophobic side chains exposed as a result of the action of the interface on the polar exterior of the molecules. 

There are no obvious structural differences between transporters from the same superfamily that function either alone or in complex vdth accessory proteins. No specific structural determinants were identified that enable a transporter to engage the accessory proteins. In contrast, periplasmic MFPs are adapted to the structural diversity of transporters. The major differences in MFPs are in the N-terminal domains and the length ofthe periplasmic coiled-coil helical regions [117]. MFPs that... 

Protein structures are so diverse that it is sometimes difficult to assign them unambiguously to particular structural classes. Such borderline cases are, in fact, useful in that they mandate precise definition of the structural classes. In the present context, several proteins have been called //-helical although, in a strict sense, they do not fit the definitions of //-helices or //-solenoids. For example, Perutz et al. (2002) proposed a water-filled nanotube model for amyloid fibrils formed as polymers of the Asp2Glni5Lys2 peptide. This model has been called //-helical (Kishimoto et al., 2004 Merlino et al., 2006), but it differs from known //-helices in that (i) it has circular coils formed by uniform deformation of the peptide //-conformation with no turns or linear //-strands, as are usually observed in //-solenoids and (ii) it envisages a tubular structure with a water-filled axial lumen instead of the water-excluding core with tightly packed side chains that is characteristic of //-solenoids. 

The two-stranded a-helical coiled coil is now recognized as one of natures favorite ways of creating a dimerization motif and has been predicted to occur in a diverse group of over 200 proteins.111 This structure consists of two amphipathic, right-handed a-helices that adopt a left-handed supercoil, analogous to a two-stranded rope where the nonpolar face of each a-helix is continually adjacent to that of the other helix. 2 This structure was first postulated by Crick to explain the X-ray diffraction pattern of a-keratin in the absence of sequence information.Pl The coiled-coil dimerization motif is natures way of creating a rod-like molecule that perhaps plays only a structural role in many fibrous proteins, such as the kmef (keratin, myosin, epidermis, fibrinogen) class 3,4 and the intermediate filament proteins)5 6 ... 

Steinert, P. M., Marekov, L. N., and Parry, D. A. D. (1993c). Diversity of intermediate filament structure Evidence that the alignment of coiled-coil molecules in vimen-tin is different from that in keratin intermediate filaments. J. Biol. Chem. 268, 24916-24925. 

The a-helix is the most abundant secondary structural element, determining the functional properties of proteins as diverse as a-keratin, hemoglobin and the transcription factor GCN4. The average length of an a-helix in proteins is approximately 17 A, corresponding to 11 amino acid residues or three a-helical turns. In short peptides, the conformational transition from random coil to a-helix is usually entropically disfavored. Nevertheless, several methods are known to induce and stabilize a-helical conformations in short peptides, including ... 

It is pertinent to consider separately the enhancement effect of salt on two steps the initiation step (onset of the flow) and the structured flow. The transport rates are related to the properties of the final structured flow and are contributed from the effects on both steps. The effect on the initiation step is clearly noticed since the critical PVP concentrations for the occurrence of the structured flow depended on the kind of salt. Effects of a salt on the cross diffusion constants of the two polymer components will be examined on both excluded volume and frictional effect. The effect on the excluded volume interaction between the two polymer components is expected to be small. This expectation is partly supported by the result that coil dimension of PVP was not influenced by the addition of a salt at 2 M in the cases of three salts LiCl, NaCl and CsCI, while these salts showed quite diverse effects on the trrmsport rates of PVP. Since viscosities vary with the kind and the concentration of salt, frictional coefficients are influenced by the presence of a salt. In this respect cross diffusion constants may be affected by salt through a change in viscosity of the medium. 

Swindells et al. [120] have calculated the intrinsic , i// propensities of the 20 amino acids from the coil regions of 85 protein structures. The distribution for coil regions is quite different than for the regular secondary structure regions, with a large increase in flP and oq conformations and much more diverse conformations in the pE and aR regions. Their results also indicate that the 18 non-Gly, Pro amino acid type are in fact quite different from each other in terms of their Ramachandran distributions, despite the fact that they are usually treated as identically distributed in prediction methods [95, 121]. Their analysis was divided into the main broad... 

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