Minimal model systems for beta sheet secondary structure in proteins.

Use of model systems to explore the forces that control beta sheet formation was stymied for many years by the perception that small increments of beta sheet necessarily aggregate. Recently, however, a number of short peptides (9-16 residues in length) that fold into two-stranded antiparallel beta sheets ('beta hairpins') have been reported; several short peptides (20-24 residues in length) that fold into three-stranded antiparallel beta sheets have also been described. These model systems are beginning to provide fundamental insights into the origins of beta sheet conformational stability.

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation.

Autonomously folding beta-hairpins have recently emerged as powerful tools for elucidating the origins of antiparallel beta-sheet folding preferences. Analysis of such model systems has suggested four potential sources of beta-sheet stability: (1) the conformational propensity of the loop segment that connects adjacent strands; (2) favorable contacts between side-chains on adjacent strands; (3) interstrand hydrogen bonds; and (4) the intrinsic beta-sheet propensities of the strand residues. We describe the design and analysis of a series of isomeric 20 residue peptides in which factors (1)-(4) are identical. Differences in beta-hairpin formation within this series demonstrate that these four factors, individually, are not sufficient to explain beta-sheet stability. In agreement with the prediction of a simple statistical mechanical model for beta-hairpin formation, our results show that the separation between the loop segment and an interstrand cluster of hydrophobic side-chains strongly influences beta-hairpin size and stability, with a smaller separation leading to greater stability.

An improved tripod amphiphile for membrane protein solubilization.

Intrinsic membrane proteins represent a large fraction of the proteins produced by living organisms and perform many crucial functions. Structural and functional characterization of membrane proteins generally requires that they be extracted from the native lipid bilayer and solubilized with a small synthetic amphiphile, for example, a detergent. We describe the development of a small molecule with a distinctive amphiphilic architecture, a "tripod amphiphile," that solubilizes both bacteriorhodopsin (BR) and bovine rhodopsin (Rho). The polar portion of this amphiphile contains an amide and an amine-oxide; small variations in this polar segment are found to have profound effects on protein solubilization properties. The optimal tripod amphiphile extracts both BR and Rho from the native membrane environments and maintains each protein in a monomeric native-like form for several weeks after delipidation. Tripod amphiphiles are designed to display greater conformational rigidity than conventional detergents, with the long-range goal of promoting membrane protein crystallization. The results reported here represent an important step toward that ultimate goal.

Non-hydrogen-bonded secondary structure in beta-peptides: evidence from circular dichroism of (S)-pyrrolidine-3-carboxylic acid oligomers and (S)-nipecotic acid oligomers.

[formula: see text] Homooligomers of beta-amino acids (S)-3-pyrrolidine-3-carboxylic acid (PCA) and (S)-nipecotic acid (Nip) were studied by circular dichroism (CD) in methanol. In each series, a profound change in the far-UV CD spectrum was observed from monomer to tetramer, but little change was observed from tetramer to hexamer. A comparable pattern is observed in the CD spectra of short proline oligomers. We conclude that both PCA and Nip oligomers with > or = four residues adopt a characteristic secondary structure.

Evaluation of hydrogen bonding complementarity between a secondary sulfonamide and an alpha-amino acid residue.

[structure: see text] We report an initial step toward the development of sulfonamide-based complements for extended peptide strands. A molecule containing one secondary sulfonamide unit and one valine residue linked by a turn-forming segment was found by IR and NMR to exhibit a doubly hydrogen-bonded folding pattern in chloroform.

Promotion of sheet formation in alpha-peptide strands by a beta-peptide reverse turn.

[structure: see text]We show that a tetrapeptide with a heterogeneous backbone, i.e., with two different classes of amino acid residues, adopts a hairpin conformation in which each type of residue plays a different structural role. The alpha-residues at the ends form hydrogen bonds characteristic of antiparallel beta-sheet secondary structure, while the central di-beta-peptide segment forms a reverse turn. The configuration of the turn residues is critical to sheet formation.

Solvent-dependent stabilization of the E configuration of propargylic secondary amides.

Secondary amides typically exist 98-99% in the Z rotamer to avoid steric repulsion between the substituent on the carbonyl carbon and the nitrogen. In contrast, secondary amide 3a displays 24% E rotamer at room temperature in aqueous solution. The analogous ester displays 6% E rotamer in chloroform, which suggests that the relatively high E conformer population observed for 3a in water results in part from the low steric bulk of the sp-hybridized carbons and in part from the hydrophobic effect.

Toward beta-peptide tertiary structure: self-association of an amphiphilic 14-helix in aqueous solution.

A major frontier in foldamer research is creation of unnatural oligomers that adopt discrete tertiary structures; at present, only biopolymers are known to fold into such compact conformations. We report an initial step toward helix-bundle tertiary structure in the beta-peptide realm by showing that a 10-residue beta-peptide designed to adopt an amphiphilic helical conformation forms small soluble aggregates in water. Sedimentation equilibrium data indicate that the aggregated state falls in the tetramer-hexamer size range. [structure: see text]

Mechanistic comparison of artificial-chaperone-assisted and unassisted refolding of urea-denatured carbonic anhydrase B.

BACKGROUND: We have previously described a method for the refolding of chemically denatured proteins in which small molecules ('artificial chaperones', a detergent and cyclodextrin) assist renaturation. In a previous analysis of lysozyme refolding from the GdmCl-denatured, DTT-reduced state, we found that enzymatic activity is regained at indistinguishable rates for unassisted (absence of additives) and artificial-chaperone-assisted refolding. While unassisted and artificial-chaperone-assisted refolding rates could also be directly compared for GdmCl-denatured bovine carbonic anhydrase B (CAB), only cationic detergents could be used as assistants. We therefore set out to determine whether artificial chaperones could assist the refolding of urea-denatured CAB, whether the charge and structure of the detergent used affects refolding assistance, and, if so, whether the assistance is mechanistically similar to that observed for GdmCl-denatured CAB. RESULTS: Our results indicate that CAB can be refolded from the urea-denatured state via the artificial chaperone process, using both anionic and cationic detergents. There is a distinctive product-determining step early in the artificial-chaperone-assisted refolding mechanism, but the rate-determining steps of the unassisted and artificial-chaperone-assisted processes are indistinguishable. CONCLUSIONS: Because the rate-determining steps of unassisted and artificial-chaperone-assisted refolding are indistinguishable, we conclude that the rate-determining step of CAB refolding is unaffected by the use of artificial chaperones. Our observations also suggest that denatured CAB undergoes a slow partial folding in concentrated urea solution.

Artificial chaperone-assisted refolding of carbonic anhydrase B.

We recently reported a new approach to protein refolding that utilizes a pair of low molecular weight folding assistants, a detergent and a cyclodextrin (Rozema, D., and Gellman, S. H. (1995) J. Am. Chem. Soc. 117, 2373-2374). Here, we provide a detailed study of carbonic anhydrase B (CAB) refolding assisted by these "artificial chaperones." When CAB is heated in the presence of a competent detergent, or when guanidinium-denatured CAB is diluted to nondenaturing guanidinium concentration in the presence of such a detergent, the detergent forms a complex with the non-native protein, thereby preventing aggregation. CAB is unable to refold from the detergent-complexed state, but folding can be induced by introduction of a cyclodextrin, which strips the detergent away from the protein. Use of artificial chaperones provides excellent yields of reactivated CAB under conditions that lead to little or no reactivation in the absence of the refolding assistants. Our studies show that the detergent can capture the unfolded protein even at submicellar concentrations, but that not all CAB-detergent complexes lead efficiently to refolded enzyme upon introduction of the stripping agent. Effective refolding appears to require that detergent stripping occur as rapidly as possible; intrinsically slow methods of detergent removal (dialysis or use of macroscopic adsorbents) are less effective than cyclodextrin at inducing renaturation upon detergent removal. The detailed characterization of artificial chaperone-assisted CAB refolding reported here should guide the application of this strategy to other proteins.

Artificial chaperone-assisted refolding of denatured-reduced lysozyme: modulation of the competition between renaturation and aggregation.

Conditions that promote renaturation of an unfolded protein also promote protein aggregation, in many cases, because these competing intramolecular and intermolecular processes are driven by similar networks of noncovalent interactions. The GroEL/GroES system and related biological chaperones facilitate the renaturation of substrate proteins by minimizing the aggregation pathway. We have devised a two-step method in which small molecules, "artificial chaperones," facilitate protein refolding from a chemically denatured state. In the first step, the protein is captured by a detergent as guanidinium chloride is diluted to a non-denaturing concentration; formation of a protein-detergent complex prevents both protein aggregation and proper refolding. In the second step, a cyclodextrin strips detergent from the protein, allowing the protein to refold. Here we describe the first application of this method to a protein that must form disulfides in the native state. Lysozyme (hen egg white) can be refolded from the Gdm-denatured, DTT-reduced state in good yields at final protein concentrations as high as 1 mg/mL with the artificial chaperone method. Several mechanistic aspects of artificial chaperone-assisted refolding have been probed, and a detailed mechanism for the kinetically controlled stripping step is proposed.

Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings.

The contributions of interstrand side chain-side chain contacts to beta-sheet stability have been examined with an autonomously folding beta-hairpin model system. RYVEV(D)PGOKILQ-NH2 ((D)P = D-proline, O = ornithine) has previously been shown to adopt a beta-hairpin conformation in aqueous solution, with a two-residue loop at D-Pro-Gly. In the present study, side chains that display interstrand NOEs (Tyr-2, Lys-9, and Leu-11) are mutated to alanine or serine, and the conformational impact of the mutations is assessed. In the beta-hairpin conformation Tyr-2 and Leu-11 are directly across from one another (non-hydrogen bonded pair). This "lateral" juxtaposition of two hydrophobic side chains appears to contribute to beta-hairpin conformational stability, which is consistent with results from other beta-sheet model studies and with statistical analyses of interstrand residue contacts in protein crystal structures. Interaction between the side chains of Tyr-2 and Lys-9 also stabilizes the beta-hairpin conformation. Tyr-2/Lys-9 is a "diagonal" interstrand juxtaposition because these residues are not directly across from one another in terms of the hydrogen bonding registry between the strands. This diagonal interaction arises from the right-handed twist that is commonly observed among beta-sheets. Evidence of diagonal side chain-side chain contacts has been observed in other autonomously folding beta-sheet model systems, but we are not aware of other efforts to determine whether a diagonal interaction contributes to beta-sheet stability.

Variations in the turn-forming characteristics of N-acyl proline units.

We have examined intramolecular hydrogen bonding in four homologous compounds, N-acetyl-, N-propionyl-, N-i-butyryl-, and N-pivaloyl-proline-methylamide, in methylene chloride, by means of 1H-nmr and ir measurements. At room temperature, the major trans conformer of MeCO-Pro-NHMe appears to be approximately 68% intramolecularly hydrogen bonded, the trans conformers of EtCO-Pro-NHMe and i-PrCO-Pro-NHMe are approximately 75% intramolecularly hydrogen bonded, and t-BuCO-Pro-NHMe is approximately 50% intramolecularly hydrogen bonded. Thus, the internally hydrogen-bonded state (C7 or gamma-turn) is significantly less populated for the N-pivaloyl compound than for the other three molecules in this series. Variable temperature measurements indicate that for each proline derivative there is very little enthalpic difference between the intramolecularly hydrogen-bonded and nonhydrogen bonded states of the trans rotamer. Changing the N-terminal acyl group also affects intramolecular hydrogen bonding (including beta-turn formation) in end-blocked Pro-Gly dipeptides.

Artificial chaperone-assisted refolding of citrate synthase.

The power of genetic engineering methods, along with increasing genomic information, makes heterologous expression of proteins an extremely important biochemical tool. Unfortunately, proteins obtained in this way often are not in their native form, and folding becomes a crucial step in protein production. We have recently developed a strategy that promotes the folding of chemically denatured proteins via the sequential addition of low molecular weight "artificial chaperones." Here we describe in detail the application of this method to porcine heart citrate synthase. Refolding yields of as high as 65% have been achieved. Mechanistic studies indicate that there are significant differences between artificial chaperone-assisted refolding of citrate synthase and artificial chaperone-assisted refolding of two other proteins that have been examined, carbonic anhydrase B (Rozema, D., and Gellman, S. H. (1996) J. Biol. Chem. 271, 3478-3487) and lysozyme (Rozema, D., and Gellman, S. H. (1996) Biochemistry 35, 15760-15771). The differences among these three test proteins reveal the range of procedural variation that must be considered in the application of the artificial chaperone method to new proteins.

Length-dependent stability and strand length limits in antiparallel beta -sheet secondary structure.

Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between alpha-helix length and alpha-helix stability, which would be impossible to probe with alpha-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel beta-sheet stability. alpha-Helices become more stable as they grow longer. Our data show that a two-stranded beta-sheet ("beta-hairpin") becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further beta-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be an intrinsic limit to strand length for most sequences in antiparallel beta-sheet secondary structure.

Residue-based control of helix shape in beta-peptide oligomers.

Proteins and RNA are unique among known polymers in their ability to adopt compact and well-defined folding patterns. These two biopolymers can perform complex chemical operations such as catalysis and highly selective recognition, and these functions are linked to folding in that the creation of an active site requires proper juxtaposition of reactive groups. So the development of new types of polymeric backbones with well-defined and predictable folding propensities ('foldamers') might lead to molecules with useful functions. The first step in foldamer development is to identify synthetic oligomers with specific secondary structural preferences. Whereas alpha-amino acids can adopt the well-known alpha-helical motif of proteins, it was shown recently that beta-peptides constructed from carefully chosen beta-amino acids can adopt a different, stable helical conformation defined by interwoven 14-membered-ring hydrogen bonds (a 14-helix; Fig. 1a). Here we report that beta-amino acids can also be used to design beta-peptides with a very different secondary structure, a 12-helix (Fig. 1a). This demonstrates that by altering the nature of beta-peptide residues, one can exert rational control over the secondary structure.