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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
J Am Chem Soc. Author manuscript; available in PMC 2010 April 21.
Published in final edited form as:
PMCID: PMC2857659
NIHMSID: NIHMS189064

Toward β-Amino Acid Proteins: A Cooperatively Folded β-Peptide Quaternary Structure

Folded polymers in nature are assembled from relatively simple building blocks but adopt complex structures through intricate networks of stabilizing noncovalent interactions. These interactions operate locally and globally to define secondary and tertiary structures, respectively. In certain cases, discrete secondary or tertiary elements associate with one another to form multi-subunit quaternary structures that can possess remarkably sophisticated functions. Nonnatural folded polymers, or foldamers, have potential for similar structural versatility. 1-4 Foldamers composed of β3-amino acids,5-8 for example (β3-peptides), can adopt stable 14-helical secondary structures in methanol6,8 or water9-15 solutions, and covalently stabilized β3-peptide dimers16 and self-assembling β3-peptide nanotubes17 have been reported. Here we describe a pair of short β3-peptides that assemble noncovalently into a well-defined quaternary structure characterized by an integral stoichiometry, highly stabilized secondary structure, and a cooperative melting transition.

Previous work has shown that appropriately designed β3-peptides can populate a secondary structure known as a 14-helix, characterized by 14-membered ring hydrogen bonds between the amide at position i and the carbonyl of position i + 2, a left-handed helical twist, and three discrete faces.6,8 Theβ3-peptide sequences studied here were chosen to increase 14-helix propensity, decrease non-specific aggregation, and favor hetero-oligomerization (Figure 1). All β3-peptides contain free N- and C-termini and an alternating pattern of positively and negatively charged side chains on one helical face to improve 14-helical structure within a monomer9,10,12 and disfavor nonspecific aggregation events reported previously.18,19 In addition, all contain β3-homoleucine residues at positions i and i + 3 and a pair of β3-homophenylalanine residues at positions 4 and 7 to favor potential interhelical interactions. Finally, each β3-peptide contains β3-homoornithine or β3-homoglutamic acid at positions 1 and 10 to favor heterodimer formation in a manner reminiscent of Fos/Jun.20 All molecules were prepared using solid-phase methods, purified to homogeneity by HPLC, and characterized by mass spectrometry, circular dichroism (CD), and analytical ultracentrifugation.21

Figure 1
Helical net representation of β3-peptides described in this work. β3-homoamino acids are identified by the single letter code used for the corresponding α-amino acids. O signifies β3-homo-ornithine.

CD spectroscopy indicated that β3-peptides Acid-1F and Base-1F are minimally 14-helical in buffered aqueous solution at a 25 μM concentration. By contrast, the CD spectrum of an equimolar mixture of Acid-1F and Base-1F at 25 μM concentration suggests a high level of 14-helix structure (Figure 2A). Analysis of the molar residue ellipticity at 210 nm (MRE210) as a function of the mole fraction (X) of Acid-1F defined a Job plot22 with a minimum at X = 0.5, suggesting that the 14-helical structure detected by CD was a hetero-oligomer containing a 1:1 ratio of Acid-1F and Base-1F (Figure 2B). This hetero-oligomer is surprisingly stable: the Tm of an equimolar mixture of Acid-1F and Base-1F at 25 μ(M is 58 °C, close to the values observed for example, for leucine zipper proteins.23,24 Sedimentation equilibrium studies indicate that whereas both Acid-1F and Base-1F are monomers at 25 μM, the equimolar mixture of Acid-1F and Base-1F is fit equally well by a monomer—hexamer equilibrium or a monomer—octamer equilibrium (Figure 2F).21,25 Moreover, the thermally induced unfolding of the hetero-oligomer is sigmoidal (Figure 2C), with a van't Hoff enthalpy of approximately 1.8 kcal·(mol·residue)−1, comparable to values measured for natural proteins (1.9–4 kcal·(mol·residue)−1).26

Figure 2
Isothermal (A,B) or temperature-dependent (C) CD analysis of Acid-1F, Base-1F, or a 1:1 mixture thereof. Sedimentation equilibrium analysis of (D) Acid-1F fit to a monomer model, (E) Base-1F fit to a monomer model, or (F) a 1:1 mixture thereof fit to ...

To probe the contribution of the β3-homoleucine side chain to bundle formation, we prepared a set of variants of Acid-1F and Base-1F in which the β3-homoleucine residues at positions 2 and 11 (Acid-1FL2,11A and Base-1FL2,11A) or 5 and 8 (Acid-1FL5,8A and Base-1FL5,8A) were substituted with β3-homoalanine (Figure 1). The CD spectrum of each Acid–Base pair–in isolation or mixed in a 1:1 molar ratio–showed modest (−7500 deg·cm2·dmol−1) values of MRE210 that were concentration-independent between 25 μM and 200 μM and resembled closely the CD spectra of the parent β3-peptides in isolation.21 Moreover, sedimentation equilibrium analysis indicated that each of the variant β-peptide was a monomer, in isolation or as a pair.21 These data suggest that formation of the hetero-oligomer demands multiple interactions along the β3-homoleucine face.

Next we made use of a widely applied disulfide exchange assay27,28 to determine whether there existed a preferred orientation of the Acid-1F and Base-1F helices within the hetero-oligomer (Figure 3). Variants of Base-1F and Acid-1F containing a single cysteine at the N- or C-terminus, respectively (Base-1FS and Acid-1FS, Figure 1), were converted into disulfide-linked homodimers (Base- 1FSSBase-1F and Acid-1FSSAcid-1F) and a heterodimer (Acid-1FSSBase-1F) followed by HPLC purification.21 The Acid-1FSSBase-1F heterodimer (Figure 3B) or a 1:1 mixture of the homodimers21 was incubated at room temperature in a redox buffer to facilitate disulfide exchange, and the reaction mixture was monitored by HPLC. As expected, at t = 5 min, the reaction starting with the Base-1FSS Acid-1F heterodimer contained only a small amount of disulfide-linked homodimers. Over the course of 24 h, however, we observed a systematic decrease in heterodimer Base-1FSS Acid-1F and a concomitant increase in homodimers Base-1FSS-Base-1F and Acid-1FSSAcid-1F. No additional changes were observed up to 72 h. Incubation of a 1:1 ratio of Base-1FSSBase-1F and Acid-1FSSAcid-1F homodimers in redox buffer generates a similar mixture of homodimers and heterodimers.21 The predominance at equilibrium of both homo- and heterodimers, irrespective of the directional approach to equilibrium, suggests a hetero-oligomer composed of both parallel and antiparallel helices whose precise arrangement must await high-resolution analysis. This work demonstrates that β3-peptides can assemble into defined, cooperatively folded, quaternary structures and constitutes an important step toward designing protein-like assemblies from nonnatural polymers.

Figure 3
(A) Equilibrium between Base-1FSSBase-1F and Acid-1FSS Acid-1F homodimers and Base-1FSS Acid-1F heterodimer under redox conditions (PBC buffer (pH 7.1) containing 500 μM reduced glutathione and 125 μM oxidized glutathione). (B) HPLC analysis ...

Supplementary Material

Supporting Information

Acknowledgment

This work was supported by the NIH (GM65453 and GM74756), the National Foundation for Cancer Research, and in part by a grant to Yale University, in support of A.S., from the Howard Hughes Medical Institute. E.J.P. was supported by NIH F32 GM076820. This paper is dedicated to Peter B. Dervan on the occasion of his 60th birthday.

Footnotes

Supporting Information Available: β-peptide synthesis, CD, analytical ultracentrifugation and disulfide exchange assays. This material is available free of charge via the Internet at http://pubs.acs.org.

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