Two-helix bundle

In a first step towards the design of / -peptides tyligomers (oligomers that fold into predictable tertiary structures [8]), carefully controlled interhelical hydrophobic interactions have been utilized to stabilize a / -peptide two-helix bundle (92) [179] (Fig. 2.17). 

Fig. 2.17 A / -peptide (92) two-helix bundle [1 79]. The parallel bundle was designed by dimerizing a 3,4-helical peptide via a disulfide bond. The interaction interface of the bundle consist of four hydrophobic residues ((S)-amino valeric acid, / -HLeu and...

Fig. 5.5 A model of conformational autocatalysis for the oligopeptide of Fig.5.4. The lowest-energy a-helical form (two-helix bundle, left-hand side) interacts with the frozen metastable (3 form (four-member (3 barrel, center). After a long Monte Carlo run (symbolized by an arrow), which consists of a million of intermediate conformations of various type, both molecules form a strong complex of two (3 type metastable forms right). During this run the a conformation unfolds and then refolds to the (3 conformation. Thus, the (3 metastable form plays a role of a catalyst in the transformation of the a native structure into the (3 form (autocatalysis)...

It turned out in the MCRE procedure that the oligopeptide molecule always attains the global minimum conformation in the form of a two-helix bundle (see Fig. 7.14a-b), if the temperature is in a certain range. Below this range, not only the two-helix bundle, but also a (very different from the latter one) four-member /6-barrel (see Fig. 7.14c), are stable. If two protein molecules interact, one of them frozen (for whatever reasons, chemical of physical) in its metastable /6-barrel conformation, while the second molecule is free to move (Fig. 7.14d), the second molecule practically always folds to the /6-barrel that interacts very strongly with the frozen /6-barrel (Fig. 7.14e). This happens even when the second molecule starts from its native (i.e., a-helical) form the a-helical form unfolds and then folds to the -barrel (Fig. 7.14e). It bas been also demonstrated that a third protein molecule, when in the presence of the two frozen /6-barrels, folds to the /6-barrel that fits very well to the two forming a stack of three /6-barrel molecules. Formation of such stacks is notorious for prion diseases. 

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... 

The tetrameric structure of the lac repressor has a quite unusual V-shape (Figure 8.22). Each arm of the V-shaped molecule is a tight dimer, which is very similar in structure to the PurR dimer and which has the two N-termi-nal DNA binding domains close together at the tip of the arm. The two dimers of the lac repressor are held together at the other end by the four carboxy-terminal a helices, which form a four-helix bundle. 

Figure 8.22 The lac repressor molecule is a V-shaped tetramer in which each arm is a dimer containing a DNA-hinding site. The helix-tum-helix motifs (red) of each dimer bind in two successive major grooves and the hinge helices (purple) bind adjacent to each other in the minor groove between the two major groove binding sites. The four subunits of the tetramer are held together by the four C-terminal helices (yellow) which form a four helix bundle. The bound DNA fragments are bent. (Adapted from M. Lewis et al., Science 271 1247-1254, 1996.)...

TFIIA also has two domains, one of which is a four-helix bundle and the other an antiparallel p sandwich. The p sandwich interacts with the N-termi-nal half of TBP and thus positions TFIIA on the other side of the complex compared with TFIIB. This domain also interacts with phosphates and sugars of DNA upstream of the TATA box. Tbe four-helix bundle domain makes no contact with DNA or TBP and is far removed from the position of TFIIB. 

Two such dimers form the tetramer through mainly hydrophobic interactions between the a helices. The p strands are on the outside of the tetramer and are not involved in the dimer-dimer interactions. The arrangement of the four a helices is unusual and provides a rare example of four a helices packed against each other in a way different from the four-helix bundle motif. 

Figure 9.17 Schematic diagram illustrating the tetrameric stmcture of the pS3 oligomerization domain. The four subunits have different colors. Each subunit has a simple structure comprising a p strand and an a helix joined by a one-residue turn. The tetramer is built up from a pair of dimers (yellow-blue and red-green). Within each dimer the p strands form a two-stranded antiparallel p sheet which provides most of the subunit interactions. The two dimers are held together by interactions between the four a helices, which are packed in a different way from a four-helix bundle. (Adapted from P.D. Jeffrey et al.. Science 267 1498-1502, 1995.)...

Figure 10.25 Structure of the dimerization region of MyoD. The a helices HI (red and brown) and H2 (light and dark green) of the two monomers form a four-helix bundle that keeps the dimer together. The loops (yellow and orange) are on the outside of the four-helix bundle. (Adapted from P.C.M. Ma et al.. Cell 77 4S1-4S9, 1994.)...

Figure 10.28 Schematic diagram of the binding of the transcription factor Max to DNA. The two monomers of Max (blue and green) form a dimer through both the helix-loop-helLx regions which form a four-helix bundle like MyoD, and the zipper regions, which are arranged in a coiled coil. The N-terminal basic regions bind to DNA in a way similar to GCN4 and MyoD. (Adapted from A.R. Ferre-D Amare et al., Nature 363 38-4S, 1993.)...

The structurally similar L and M subunits are related by a pseudo-twofold symmetry axis through the core, between the helices of the four-helix bundle motif. The photosynthetic pigments are bound to these subunits, most of them to the transmembrane helices, and they are also related by the same twofold symmetry axis (Figure 12.15). The pigments are arranged so that they form two possible pathways for electron transfer across the membrane, one on each side of the symmetry axis. 

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. 

Figure 13.18 Ribbon diagram of the structure of human growth hormone. The fold is a four-helix bundle with up-up-down-down topology, and consequently there are two long cross-connections between helices A and B as well as between helices C and D. (Adapted from J. Wells et al., Annu. Rev. Biochem.

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

They started from the sequence of a domain, Bl, from an IgG-binding protein called Protein G. This domain of 56 amino acid residues folds into a four-stranded p sheet and one a helix (Figure 17.16). Their aim was to convert this structure into an all a-helical structure similar to that of Rop (see Chapter 3). Each subunit of Rop is 63 amino acids long and folds into two a helices connected by a short loop. The last seven residues are unstructured and were not considered in the design procedure. Two subunits of Rop form a four-helix bundle (Figure 17.16). 

Fig. 9. An overall view of the Fepr molecule from D. vulgaris showing the three domains. Domain 1 is predominantly a-helical and contains an unusual configuration of two three-helix bundles approximately perpendicular to one another (see Fig. 11). Domains 2 and 3 have central /3-sheets surrounded by helices. The two Fe-S clusters are at the center of the figure the hybrid cluster is on the left, and located near the interfaces of the three domains.

In 1996, the 3D-structure of D. vulgaris Rr was published by de-Mare and collaborators 48), and all the studies earlier published were proved to be correct. The protein is described as a tetramer of two-domain subunits (Fig. 4). Each subunit contains a domain characterized by a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like Fe(RS)4 domain (see Fig. 2). In this last do-... 

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