Orientation of a-helices

Fig. 17. Effect of the orientation of a helical structure on the position of the amide I band adapted from Cornut et al. [98]. Variation of the amide I band wavenumber maximum on the PM-IRRAS spectra as a function of the 6 tilt angle of the a-helix is shown. 9 is the tilt angle between the helical axis and the normal to the interface. Taken from Ref. [107] with permission from American Chemical Society.

Donnelly, D., Overington, J. P, Blundell, T. L. The prediction and orientation of a-helices from sequence alignments the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules Prot. Engng. 1994 7, 645-653. 

Two methods have been used to determine the secondary structure and orientation of membrane proteins in supported bilayers polarized ATR-FTIR spectroscopy and oriented CD spectroscopy. SFVS may also be applied to study peptide and protein structures in supported bilayers. Polarized ATR-FTIR spectroscopy is sensitive enough that high-quality spectra can be obtained from a single bilayer. Beta-sheet structures are readily distinguished from a-helical and random stmctures, and the orientations of a-helices are determined from the linear dichroism of the peptide amide 1 bands (20). Multiple stacks of supported bilayers have to be used to gain enough sensitivity to determine the stmcture and orientation of a-helices in lipid bilayers by oriented CD spectroscopy (60, 93). 

For a given secondary structure of the peptide, the shape of the dipolar curve is characteristic of the peptide tilt. Figure 18.6 shows the theoretical dipolar curves for a surface-bound S-state (x 90°), an inserted I-state (x = 0°), and a tilted T-state (0° < x < 90°) orientation of a helical peptide. The positions in the x/p-plot corresponding to the different states are indicated. (For exact values of x and p used in the calculations, see the figure legend.) It can be noted that the curve in Figure 18.6a is very similar to the curve of Figure 18.5b, both of which correspond to an S-state orientation of the peptide. 

Orientational constraints have been collected for a wide variety of molecular systems from synthetic polymers [32, 33] to structural proteins, such as silk [34, 35]. Orientational constraints have also been collected for retinal bound to bacteriorhodopsin [36], suggesting a host of ligand receptor systems that might be studied. Orientational constraints have been collected on other synthetic and biosynthetic polypeptides in bilayer environments, such as Magainin-2, a toxin from frog skin [37], the M2 8 from the acetylcholine receptor [38] and M2-TMP from Influenza A virus [39]. Such studies have led to a description of the orientation of a-helices relative to the bilayer. Proteins such as the fd and Pfl bacteriophage coat proteins have also been... 

Fig. 15.8. Schematic representation of the orientation of a helices at the common packing angles. The dihedral angle is positive if the second helix (behind) is obtained by clockwise rotation of the first (in front)...

Membrane proteins often contain a-helical sections. We have developed a method called oriented circular dichroism (OCD see reference 1), which can be used to determine the orientation of a-helices with respect to the plane of the membrane. This method is simple and easy to use compared with, for example, the NMR method, which requires isotope labeled samples. Indeed, it is the ease of this method that allowed us to examine alamethicin in many different chemical conditions and that resolved a controversial question about the nonconducting state of alamethicin and subsequently led to the discovery of a new phenomenon of amphiphilic helical peptides (2). 

Huschilt JC, Millman BM, Davis JH (1989) Orientation of a-helical peptides in a lipid bilayer. Biochim Biophys Acta 979(1) 139-141... 

The conformation of peptides on surfaces has been studied by reflection absorption Fourier transform infrared spectroscopy. The two amide bond signals present in the IR spectra provide information about the secondary structure of the peptide as well as the orientation of a helical peptide with respect to the surface (Koga et al., 2006 Yasutomi et al., 2004,2005). 

TABLE I. Orientation of a-helices in LMH and LM reaction centers. The average was obtained from five different samples for each type of preparation. 

Figure 3.S Schematic diagram of packing side chains In the hydrophobic core of colled-coll structures according to the "knobs In holes" model. The positions of the side chains along the surface of the cylindrical a helix Is pro-jected onto a plane parallel with the heUcal axis for both a helices of the coiled-coil. (a) Projected positions of side chains in helix 1. (b) Projected positions of side chains in helix 2. (c) Superposition of (a) and (b) using the relative orientation of the helices In the coiled-coil structure. The side-chain positions of the first helix, the "knobs," superimpose between the side-chain positions In the second helix, the "holes." The green shading outlines a d-resldue (leucine) from helix 1 surrounded by four side chains from helix 2, and the brown shading outlines an a-resldue (usually hydrophobic) from helix 1 surrounded by four side chains from helix 2.

Coiling of a helices in a-keratins. Residues on the same side of an a helix form rows that are tilted relative to the helix axis. Packing helices together in fibers is optimized when the individual helices wrap around each other so that rows of residues pack together along the fiber axis. Helices in coiled coil (c) are oriented in parallel. 

Another versatile approach for the creation of artificial four-helix-bundle proteins (Scheme 21) is the assembly of a-helical peptide units via selective disulfide cross-linking, which allows for an arbitrary combination, arrangement, and orientation of the helices.[127 129]... 

Coiled coils are bundles of a-helices that are wound into superhelical structures (Fig. 1). Most commonly, they consist of two, three, or four helices, running in the same (parallel) or in opposite (antiparallel) directions, but structures with five and more helices have been determined. They are usually oligomers either of the same (homo) or of different chains (hetero), but on occasion consist of consecutive helices from the same polypeptide chain, which in that case almost always have an antiparallel orientation. 

It has been found out that the structure of proteins is flexible and there are many differences between the static spatial image of a protein and a dynamic view of its structure. This divergence is caused by the fact that the repetitive part of a-helices and [3-strands of protein folds, often described as a succession of secondary structures, can assume different local spatial orientation. Two experimental methods can be used to measure the flexibility in precise regions of protein structures (the anatomic mean square displacement, B-factor, measured during crystallographic experiments, and indirectly by NMR experiments which show different local conformation that could correspond directly to different stages of protein structures) (Bornot et al., 2007). 

Fig. 17 shows the effects of the orientation of a-helix structures on the position of the amide I band [107], It is adapted from calculated spectra in the amide I and II regions for pure a-helices when changing the tilt angle [98]. If the helix tilt angle is varied from 0° (a-helix perpendicular to the interface) to 90° (a-helix parallel to the interface), the amide I band position should shift from 1656 to 1649 cm-1. Therefore, changes in the orientation of a-helix structure may cause the shift of the amide I band, as well as the intensity ratio of amide land II. 

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