De Novo Design of a Monomeric Helical β-Peptide Stabilized by Electrostatic Interactions

Cheng, Richard P.; DeGrado, William F.

doi:10.1021/ja010438e

Cited by 108 publications

(106 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…␣/␤-Peptides 5 and 6 represent an improvement in gp41 mimicry relative to 4 (vide supra), but it would be desirable to place ␤-residues throughout an ␣/␤-peptide sequence to maximize resistance to proteolysis (30)(31)(32). Each ␣3␤ 3 replacement, however, adds a flexible bond to the backbone, which should increase the conformational entropy penalty associated with helix formation (26,33,34). The greater conformational entropy of the unfolded state of 4 relative to 3, arising from eleven ␣3␤ 3 replacements, may account for the large difference in binding affinity for gp41-5 between these two oligomers.…”

Section: First Generation ␣/␤-Peptide Gp41 Mimic Designs and In Vitromentioning

confidence: 99%

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Horne

Johnson

Ketas

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

254

269

View full text Add to dashboard Cite

Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important proteinprotein interactions. Here we evaluate an approach based on combining ␣-and ␤-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that ␣/␤-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virusinfectivity assays collectively indicate that the gp41-mimetic ␣/␤-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived ␣-peptides. An optimized ␣/␤-peptide is far less susceptible to proteolytic degradation than is an analogous ␣-peptide. Our findings show how a two-stage design approach, in which sequence-based ␣3␤ replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.alpha/beta-peptides ͉ HIV ͉ protein folding ͉ protein-protein interactions I dentification of strategies for interference with specific biopolymer recognition processes constitutes a fundamental challenge. Protein-protein associations are often resistant to inhibition by small molecules because the contact surfaces on the natural partners are large (1). Current clinical approaches to inhibiting proteinprotein interactions that underlie viral infection or aberrant signaling at the cell surface are based on the use of medium-length peptides or proteins (2). It would be valuable to identify alternative sources of antagonists for this type of protein recognition event.Here we show that peptide-like oligomers with unnatural backbones can function as potent antiviral agents by blocking a key protein-protein interaction. The design strategy we employ may prove general for ␣-helix mimicry.The HIV membrane protein gp41 mediates viral envelope-host cell membrane fusion, an essential step in the viral infection cycle. During HIV cell entry, the N-terminal fusion segment of trimeric gp41 inserts into the host cell membrane (3). A profound structural rearrangement of gp41 ensues, driven by formation of an antiparallel six-helix bundle (4-6), which leads to juxtaposition of the viral and host cell membranes. The prehairpin fusion intermediate is composed of three copies of gp41 in an extended conformation. The so-called ''class I'' fusion mechanism used by HIV is common to a variety of enveloped viruses, including those responsible for influenza, Ebola, and SARS (7,8). A number of ␣-peptides based on sequences from the gp41 N-terminal heptad repeat (NHR) domain or C-heptad repeat (CHR) domain (e.g., Fig. 1B, 1 and 2) have been investigated as anti-HIV agents (9, 10). These compounds are thought to act by binding to a gp41 prehairpin intermediate, thereby preventing six-helix bundle formation and subsequent virus-cell fusion. The drug enfu...

show abstract

Section: First Generation ␣/␤-Peptide Gp41 Mimic Designs and In Vitromentioning

confidence: 99%

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Horne

Johnson

Ketas

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

254

269

View full text Add to dashboard Cite

show abstract

“…44 Previously, β-peptides with 14-helical structure stabilized by electrostatic interactions have been shown to unfold in the presence of high salt, in accordance with this principle. 25 To provide additional evidence that electrostatic interactions contribute to the stabilities of the β-peptides studied here, we monitored the effects of increasing concentrations of NaCl on the structure of peptides 2 and 2-I6. Figure 6 illustrates the relationship between the mean residue ellipticity at 214 nm (Θ 214 ) of these two β-peptides and salt concentration from 0 to 2.25 M. The shallow sigmoidal shape of the curves has been observed in other salt-bridge-stabilized β-peptides 25 and demonstrates that screening of electrostatic interactions destabilizes the 14-helix.…”

Section: Electrostatic Screeningmentioning

confidence: 99%

Relationship between Side Chain Structure and 14-Helix Stability of β³-Peptides in Water

et al. 2004

View full text Add to dashboard Cite

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, β 3 -peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that β 3 -amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in β 3 -peptides containing β 3 -homoserine or β 3 -homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas-and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of β 3 -amino acids differ starkly from the α-helix propensities of analogous α-amino acids. This contrast informs current models for α-helix folding, and suggests that 14-helix folding is governed by radically different biophysical forces than is α-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical β-peptide ligands for macromolecular targets.Folded polymers are used in Nature for virtually every vital process, from catalysis to information storage, from cellular signaling to molecular transport. Nonnatural folded polymers, or foldamers, 1 have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. [1][2][3] Previous studies of natural polymers -peptides, proteins, and nucleic acids -have shown that polymer folding is an extremely subtle process, governed by countless interactions among the backbone, side chains, and solvent. Nevertheless, control of foldamer structure is crucial if these molecules are to realize their full potential as tools in biology and medicine.A key element of foldamer design is therefore the ability to predict the folded structure of a given backbone and modulate this structure by altering the backbone and/or side chains. 1,3 In this respect, β-peptides are perhaps the best-characterized foldamers, as they populate a wide array of secondary structures including helices, sheets, and reverse turns. 1,4,5 are named for the number of atoms in a hydrogen-bonded ring and include the 10-helix, the 10/12-helix, the 12-helix, and the 14-helix ( Figure 1A). Helix type is largely determined by choice of β-amino acid monomer: cyclic ring constraints within the monomer of four atoms, five atoms, or six atoms promote the 10-helix, 12-helix, and 14-helix, respectively, 6-9 while acyclic, monosubstituted residues (β 2 -and β 3 -residues) te...

show abstract

“…[9][10][11][12] When properly designed, β 3 -peptides assemble into stable, monomeric, 3 14 -helical structures in water, a first step toward formation of stable quaternary structures. Structural features that promote stable 3 14 -helices include alternating cationic and anionic side chains arranged on one helical face to support salt bridge formation [13][14][15] and arranged to minimize the helix macrodipole. 12,16,17 Indeed, β 3 -peptides that embody these features tolerate extensive substitution of the remaining two helix faces 12,17,18 to generate highly protease-resistant 19 molecules that inhibit interactions between proteins both in vitro 18,20,21 and in cell-based assays.…”

Section: Introductionmentioning

confidence: 99%

“…29 Disulfide bond formation between two β-peptide monomers generated a covalent β-peptide dimer that underwent a cooperative melting transition. 29,30 Recently, we discovered that β-peptides containing alternating cationic and anionic side chains arranged on one helical face 13,14 and β-homoleucine residues on a second face assemble into helical oligomers that we refer to as β-peptide bundles. [31][32][33] The β-peptide bundles formed from the sequences Zwit-1F, its iodinated analogue Zwit-1F*, and the 1:1 mixture of Acid-1F and Base-1F ( Figure 1) were characterized extensively using biophysicalmethodsandhighresolutionstructuredetermination.…”

Section: Introductionmentioning

confidence: 99%

Biophysical and Structural Characterization of a Robust Octameric β-Peptide Bundle

et al. 2007

View full text Add to dashboard Cite

Proteins composed of α-amino acids are essential components of the machinery required for life. Stanley Miller's renowned electric discharge experiment provided evidence that an environment of methane, ammonia, water, and hydrogen was sufficient to produce α-amino acids. This reaction also generated other potential protein building blocks such as the β-amino acid β-glycine (also known as β-alanine); however, the potential of these species to form complex ordered structures that support functional roles has not been widely investigated. In this report we apply a variety of biophysical techniques, including circular dichroism, differential scanning calorimetry, analytical ultracentrifugation, NMR and X-ray crystallography, to characterize the oligomerization of two 12-mer β 3 -peptides, Acid-1Y and Acid-1Y*. Like the previously reported β 3 -peptide Zwit-1F, Acid-1Y and Acid-1Y* fold spontaneously into discrete, octameric quaternary structures that we refer to as β-peptide bundles. Surprisingly, the Acid-1Y octamer is more stable than the analogous Zwit-1F octamer, in terms of both its thermodynamics and kinetics of unfolding. The structure of Acid-1Y, reported here to 2.3 Å resolution, provides intriguing hypotheses for the increase in stability. To summarize, in this work we provide additional evidence that nonnatural β-peptide oligomers can assemble into cooperatively folded structures with potential application in enzyme design, and as medical tools and nanomaterials. Furthermore, these studies suggest that nature's selection of α-amino acid precursors was not based solely on their ability to assemble into stable oligomeric structures.

show abstract

De Novo Design of a Monomeric Helical β-Peptide Stabilized by Electrostatic Interactions

Cited by 108 publications

References 31 publications

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Relationship between Side Chain Structure and 14-Helix Stability of β³-Peptides in Water

Biophysical and Structural Characterization of a Robust Octameric β-Peptide Bundle

Contact Info

Product

Resources

About

De Novo Design of a Monomeric Helical β-Peptide Stabilized by Electrostatic Interactions

Cited by 108 publications

References 31 publications

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Relationship between Side Chain Structure and 14-Helix Stability of β3-Peptides in Water

Biophysical and Structural Characterization of a Robust Octameric β-Peptide Bundle

Contact Info

Product

Resources

About

Relationship between Side Chain Structure and 14-Helix Stability of β³-Peptides in Water