A-helix bundle

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

Presnell, S.R., Cohen, EE. Topological distribution of four-a-helix bundles. Proc. Natl. Acad. Sci. USA 86 6592-6596, 1989. 

A helix bundle is a protein composed of a series of rodlike helical domains linked by flexible segments and inserted into a membrane to form a cluster of helices roughly parallel to one another and perpendicular to the plane of the membrane. 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

Chou K-C, Maggiora GM, Nemethy G, Scheraga HA. Energetics of the structure of the four-a-helix bundle in proteins. Proc Natl Acad Sci USA 85 1988 4295-4299. 

Membranes contain many largely a-helical proteins. Cell surface receptors often appear to have one, two, or several membrane-spanning helices (see Chapter 8). The single peptide chain of the bacterial light-operated ion pump bacteriorhodopsin (Fig. 23-45) folds back upon itself to form seven helical rods just long enough to span the bacterial membrane in which it functions.189 Photosynthetic reaction centers contain an a helix bundle which is formed from two different protein subunits (Fig. 23-31).190 A recently discovered a,a barrel contains 12 helices. Six parallel helices form an inner barrel and 6 helices antiparallel to the first 6 form an outer layer (see Fig. 2-29).191-193... 

On the other hand, pyrenyl-L-alanine 184 has also been used as a conformational probe in the characterization of an artificial 4-a-helix bundle protein.11,121 The 53-residue peptide 186 incorporating one residue of 184 in each of two different helical segments was synthesized by solid-phase synthesis using a segment condensation strategy and the oxime resin. Boc-pyrenyl-L-alanine 191 was coupled just like any other amino acid by the BOP/HOBt method in DMF. CD and fluorescence studies demonstrated that the two pyrene groups were in close proximity forming an excimer complex, which is possible only when the polypeptide chain folds into a 4-a-helix bundle structure. 

Along the same lines, an artificial ion channel was prepared by Montal and coworkers [33] using the TASP approach. In their work, a four a-helix bundle structure 67 was synthesized on a peptide template. The ion transport ability was well characterized and 67 turned out to have several similarities with the natural acetylcholine receptor channel they were mimicking. 

The development of synthetic enzymes and proteins has also been achieved through the preparation of structurally defined peptide nanostructures. A nice example, reported by DeGrado and co workers [67], is the construction (Fig. 27) of a four a-helix bundle system (72) that was shown to complex four metalloporphyrins by their axial coordination with the imidazole of the properly oriented histidines. This type of structure could be used as an artificial photosynthetic center. Along the same lines, Benson and co-workers [68] recently prepared a miniature hemoprotein, 73, by linking two units of a 13-amino acid peptide to a porphyrin. UV-visible and CD studies confirmed that the metalloporphyrin is indeed sandwiched between the a-helical peptides, as depicted in 73. 

From a totally different point of view, Morii and co-workers [70] have studied the utility of synthetic proteins as chiral hosts. They showed that a-helix bundle structures, formed by the folding of peptides such as 75, induced chirality in fluorescent dyes by forming inclusion complexes in the hydrophobic interior of the structures. Again these results can have implications for the development of optical materials and switches. 

An a-helix bundle may become a second-order cooperative folding unit if the interaction energy terms are such that the intermediate terms in the partition function become negligibly small [Eq. (14)] and the entire partition function reduces to a two-state partition function (i.e., a partition function of the form 1 + e G/RT). If such is the case, the a-helix bundle will be either completely folded or unfolded. Higher order cooperative folding units can be constructed from lower order ones following the same rules. The most immediate application of this approach is to proteins exhibiting pure a-helical structural motifs. 

One of the most striking features of the rhodopsin structure is the complexity and compactness of a helix bundle cap or plug formed from the extracellular interhelix loops and N-terminal segment (19). Together, the N-terminal... 

Shifman JM, Gibney BR, Sharp RE et al (2000) Heme redox potential control in de novo designed four-a-helix bundle proteins. Biochemistry 39 14813-14821... 

For proteins with multiple transmembrane domains, it is not necessary to have exclusively hydrophobic amino acids a pair of amino acids with opposite charges may be present in the lipophilic environment of the membrane. Therefore a search for amphipathic a-helices must be undertaken. Amphipathic helices have well-defined hydrophobic character, the hydrophobic face which would project towards the membrane/lipid environment, and a hydrophilic face, which would project out into the aqueous phase or towards the core of a helix bundle. Often times the distinction is not clear and there are regions of mixed hydrophobic/hydrophilic character. Graphically this can be realized with a helical-wheel representation in which the amino acid side chains project out, at 100 degree intervals, from the view along the long, helical axis. 

Cry, Cyt, and Vip toxins are all composed of three domains. Figure 4.13 shows the three-dimensional structure of CrylAa, Cry3Aa toxins, and Cry2Aa protoxin. Domain I is a seven a-helix bundle in which a central helix a-5 is surrounded by six outer helices. This domain has been implicated in the formation of ion channel in the membrane. Domain II, which consists of three antiparallel (i-sheets packed around a hydrophobic core, represents the most divergent part in structure among Cry toxin molecules and is believed to determine insect specificity. Finally, domain III, which is a 3-sandwich of two antiparallel P-sheets, determines receptor binding (see review by Bravo et al., 2005). 

Some natural ion channels are believed to form amphiphilic a-helix bundles in hydrophobic lipid membranes, where the a-helices assemble with their hydrophilic parts facing each other, resulting in a hydrophilic channel. If artificial peptides that had appropriate combinations of both hydrophobic amino acid residues and hydrophobic amino acid sequences were used, the peptides would self-assemble to form a hydrophilic pathway in the lipid membrane. 

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