Four-helix bundle structures

In most four-helix bundle structures, including those shown in Figure 3.7, the a helices are packed against each other according to the "ridges in grooves" model discussed later in this chapter. However, there are also examples where coiled-coil dimers packed by the "knobs in holes" model participate in four-helix bundle structures. A particularly simple illustrative example is the Rop protein, a small RNA-binding protein that is encoded by certain plasmids and is involved in plasmid replication. The monomeric sub unit of Rop is a polypeptide chain of 63 amino acids built up from two... 

Figure 3.7 The polypeptide chains of cytochrome bs62 and human growth hormone both form four-helix-bundle structures.

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

Like other hormones in this class of cytokines, GH has a four-helix bundle structure as described in Chapter 3 (see Figures 3.7 and 13.18). Two of the a helices, A and D, are long (around 30 residues) and the other two are about 10 residues shorter. Similar to other four-helix bundle structures, the internal core of the bundle is made up almost exclusively of hydrophobic residues. The topology of the bundle is up-up-down-down with two cross-over connections from one end of the bundle to the other, linking helix A with B and helix C with D (see Figure 13.18). Two short additional helices are in the first cross-over connection and a further one in the loop connecting helices C and D. 

Fig. 6. The high-resolution NMR structure of 2D, a 35-residue designed polypeptide that forms a four-helix bundle structure, showing the location of the aromatic residues in the core of the folded motif The cartoon illustrates the unexpected fold of a2D where the hairpin subunits dimerize in a interleaved mode. Reproduced with permission from J Am Chem Soc (1998) 120 1138. ( 1998 ACS)...

A third group of lipid-binding proteins have a four-helix bundle structure. They include the insect lipophorins, which transport diacylglycerols in the hemolymph (see main text), and nonspecific lipid carriers of green plants.q An 87-residue four-helix protein with a more open structure binds acyl-coenzyme A molecules in liver.r... 

More relevant for this section is the use of porphyrins as template for the construction of de novo metalloproteins. Indeed, the attachment of helical peptide units to these templates creates four-helix bundle structures that have been used as an artificial ion channel 2 or a hydroxylase enzymeJ33,34 In these cases, the peptide units were coupled to the template by using the HOSu or the TBTU methods. As illustrated in Scheme 10 starting from 33, formation of the tetrasuccimidyl ester 34 and attachment of the protected peptide unit 35 gives 36 and this is followed by deprotection to 37. 

Fig. 17. An incremental approach to the design of a four-helix bundle protein (Ho and DeGrado, 1987). (a) The sequence of a peptide is first optimized for forming a very stable tetramer of a helices. The stability of the tetramer can be assessed from the dissociation constant for the cooperative monomer-to-tetramer equilibrium, (b) Two optimized helical sequences are then connected in a head-to-tail manner by a single loop. The loop sequence can be optimized by evaluating a series of alternate designs, (c) Finally, the entire four-helix bundle structure can be constructed from four optimized helices and three optimized loops.

The helical content of the tetramers formed by all three peptides was approximately 70%, a value consistent with the proposed four-helix bundle structure. The stabilities of the tetramers depended both on chain... 

Salt Bridges in Four-Helix Bundle Structures of Apolipoprotein E3 22-kDa Fragments... 

Fig. 17. Model of the interaction of the four-helix bundle structure of the apoE3 22-kDa fragment with lipid. The four-helix bundle structure as it exists in solution is shown on the left. On the right, in the presence of lipid, the bundle opens without disrupting a helices, exposing the hydrophobic core of the bundle and making it available to interact with lipid (Weisgraber el ai, 1992).

Fig. 18. Three possibilities for the orientation of the four-helix bundle structure of the apoES 22-kDa fragment at an air-water interface. The calculated molecular area of each orientation based on the bundle dimension in Fig. 16 is indicated above each structure.

Yes. Most cytokines have a common four-helix bundle structure. Experimental techniques including scanning alanine mutagenesis have been used to show that cytokines have several regions that are recognized by their receptors. Therefore, one cytokine molecule can act to cross-link two separate receptor molecules. 

We have made efforts to produce protein nano-fiber using arbitrary proteins fibers kept in native structures. Thereby, we expect to construct functional fibers because the binding units retain the native structures. By inducing mutations in a pair of adaptor proteins, hydrophobic and electrostatic interactions can be modified. By mixing the resulting two proteins, fiber will be formed spontaneously (Fig. 33.1). We expect that the protein-protein interaction will be formed through the interaction between two ot-helices of one protein and two a-helices of another protein, thus resulting in a four-helix bundle structure [3]. 

LARFH is an artificial protein designed previously (Akanuma and Yamagishi) by mimicking C-terminal four-helix bundle domain of Escherichia coli [4]. LARFH forms a monomeric four-helix bundle structure and shows high thermal stability. 

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