Helix bundle peptide

Horseman ND Yu-Lee LY (1994) Transcriptional regulation by the helix bundle peptide hormones growth hormone, prolactin, and hematopoietic cytokines. Endocrinol Rev, 15 627-649. 

Razeghifard AR, and Wydrzynski T. Binding of Zn-chlorin to a synthetic four-helix bundle peptide through histidine ligation. Biochemistry 2003 42 1024-1030. 

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... 

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,...

Early biochemical studies supported the hypothesis that the HRl and the HR2 peptides would interact to form a helical structure (Chen et al. 1995 Lu et al. 1995). This hypothesis was strengthened when X-ray structures were resolved for co-crystals of HRl and HR2 peptides (Chan et al. 1997 Tan et al. 1997 Weissenhom et al. 1997). The results showed that in the six-helix bundle, three HRl domains were packed tightly together in the center of the bundle, with the HR2 domains bound in an antiparallel manner in grooves formed along the HRl core. 

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...

Baltzer and co-workers have utilized a synthetic peptide scaffold to incorporate features of transaminase enzymes [ 13]. Using this approach, they have attempted to achieve the selective and tight binding of a pyridoxal phosphate coenzyme observed in transaminase enzymes. A synthetic helix-turn-helix peptide known to dimerize into a four-helix bundle was chosen as the platform for design [5]. 

The helix-turn-helix scaffold is designed to dimerize into a four-helix bundle. Modification of the peptide with the nicotinoyl functionality did not significantly perturb the peptide structure. CD spectroscopy showed no loss in helici-ty from the parent peptide and NMR spectroscopy confirmed successful incorporation of the nicotinoyl group as well as maintenance of crucial NOE connectivities. In particular, the presence of long-range NOE signals between the side chains of phenylalanine 38 and leucine 12 or isoleucine 9, which lie near the C- and AT-termini, respectively, demonstrate that the supersecondary structure of the motif has been conserved. 

Flg.1. In the amino acid sequence of KO-42 is encoded its fold and its function as it controls the formation of a hairpin helix-loop-helix motif that dimerizes to form a four-helix bundle. On the surface of the folded motif a reactive site is formed that catalyzes hydrolysis, transesterification and amidation reactions of reactive esters, whereas unfolded peptides are incapable of cooperative catalysis. In addition the values, and thus the reactivities, of the histidine residues are controlled by the fold. The pK of each His residue of KO-42 is shown in the figure and deviate by as much as 1.2 units from that of random coil peptides which is 6.4... 

The 42-residue peptide KO-42 folds in solution into a hairpin helix-loop-helix motif that dimerizes to form a four-helix bundle. On the surface of the folded motif there are six histidines with assigned piC values in the range 5.2 to 7.2 (Fig. 1) and the second-order rate constant for the hydrolysis of mono-p-nitro-phenyl fumarate is 1140 times larger than that of the 4-methylimidazole-cataly-zed reaction at pH 4.1 and 290 K [13]. The reaction mechanism was found to be pH dependent as the kinetic solvent isotope effect was 2.0 at pH 4.7 and 1.0 at pH 6.1 and the pH dependence showed that the reaction rate depended on residues in their unprotonated form with piCj, values around 5. It was thus established that there are functional cooperative reactive sites that contain protonated and unprotonated His residues. 

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. 

Fig. 16. Schematic representation of the assembly of designed heme protein SAMs on silanized quartz substrates. Designed peptides are synthesized, homodimerized, and selfassociate to form four-helix bundles prior to heme incorporation, followed by chemisorption on prepared quartz surfaces. Reprinted with permission from Ref. (185) copyright 1998 American Chemical Society.

Helix bundles. A third peptide chain can be added to a coiled coil to form a triple-stranded bundle.180-183 An example is the glycoprotein laminin found in basement membranes. It consists of three peptide chains which, for -600 residues at their C-terminal ends, form a three-stranded coil with heptad repeats.182184 Numerous proteins are folded into four helical segments that associate as four-helix bundles (Fig. 2-22).185-188 These include electron carriers, hormones, and structural proteins. The four-helix bundle not only is a simple packing arrangement, but also allows interactions between the + and - ends of the macro-dipoles of the helices. 

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... 

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. 

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. 

On the other hand, Futaki and Kitagawa [19] prepared a four-helix bundle protein that was also stabilized by disulfide bonds. However, in this case, they synthesized the artificial protein with its four different peptide structures (I, II, III, IV) by selectively forming the disulfide bonds, as illustrated in Fig. 11. 

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