Design of a Monomeric 23-Residue Polypeptide with Defined Tertiary Structure

Struthers, Mary; Cheng, Richard P.; Imperiali, Barbara

doi:10.1126/science.271.5247.342

Cited by 304 publications

(229 citation statements)

References 33 publications

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“…From both CD and NMR data, @pep-3, which contains the tight-turn-forming sequence YDWKV (Varnum et al, 1993), is observed to induce a greater population of @-sheet than found in @pep-2. This apparent turn-induced increase in conformational stability also has been observed in a designed 23-residue +peptide simply by shifting from a type-I1 to type-11' @-turn motif (Struthers et al, 1996). There, however, aggregation apparently was not inducing folding.…”

Section: K H Muyo Et Ulsupporting

confidence: 62%

A recipe for designing water‐soluble, β‐sheet‐forming peptides

1996

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Based on observations of solubility and folding properties of peptide 33-mers derived from the &sheet domains of platelet factor-4 (PF4), interleukin-8 (IL-8), and growth related protein (Gro-a), as well as other 6-sheet-forming peptides, general guidelines have been developed to aid in the design of water soluble, self-association-induced 0-sheet-forming peptides. CD, 'H-NMR, and pulsed field gradient NMR self-diffusion measurements have been used to assess the degree of folding and state of aggregation. PF4 peptide forms native-like @-sheet tetramers and is sparingly soluble above pH 6. IL-8 peptide is insoluble between pH 4.5 and pH 7.5, yet forms stable, nativelike &sheet dimers at higher pH. Gro-a peptide is soluble at all pH values, yet displays no discernable @-sheet structure even when diffusion data indicate dimer-tetramer aggregation. A recipe used in the de novo design of water-soluble 0-sheet-forming peptides calls for the peptide to contain 40-50~0 hydrophobic residues, usually aliphatic ones (I, L, V, A, M) (appropriately paired and mostly but not always alternating with polar residues in the sheet sequence), a positively charged (K, R) to negatively charged (E, D) residue ratio between 4/2 and 6/2, and a noncharged polar residue (N, Q, T, S) composition of about 20% or less. Results on four de novo designed, 33-residue peptides are presented supporting this approach; Under near physiologic conditions, all four peptides are soluble, form &sheet structures to varying degrees, and self-associate. One peptide folds as a stable, compact 0-sheet tetramer, whereas the others are transient 6-sheet-containing aggregates.

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Section: K H Muyo Et Ulsupporting

confidence: 62%

A recipe for designing water‐soluble, β‐sheet‐forming peptides

1996

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“…Unfortunately, initial attempts to design proteins led to structures that formed molten globulelike states with dynamic behavior relative to natural proteins. More recently, it has been possible to design small uniquely folded proteins that incorporate all of the commonly occurring secondary structural and supersecondary structural motifs (29)(30)(31)(32)(33)(34)(35)(36). These studies illustrated the delicate interplay of forces that define the uniquely folded structures of proteins; hydrophobicity provides a strong driving force for folding, but designs based on this consideration alone often adopt dynamically averaging Abbreviations: DF1, Due Ferro 1; PDB, Protein Data Bank.…”

mentioning

confidence: 99%

Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins

Lombardi

Summa

Geremia

et al. 2000

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

232

279

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De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 Å rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the GluXxx-Xxx-His class of dinuclear metalloproteins. This protein was synthesized and structurally characterized as the di-Zn(II) complex by x-ray crystallography, by using data that extend to 2.5 Å. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs. The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands. The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands. In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation. P roteins use a limited repertoire of metal ion cofactors to help catalyze a multitude of reactions. For example, diiron sites (1-4) mediate reversible oxygen binding in hemerythrins, whereas they function as hydrolytic centers in phosphatases. Structurally similar diiron sites also mediate a number of oxygendependent oxidative processes. Ferritins serve as ferroxidases, while other diiron proteins catalyze hydroxylation, epoxidation, and desaturation reactions. Further, a diiron site in Escherichia coli ribonucleotide reductase is responsible for the formation of a Tyr radical. How do the structures of these proteins tune the chemical properties of a common diiron center to obtain such a diversity of highly specific catalysts? This question is being addressed through the study of the natural proteins as well as the study of small-molecule diiron complexes (1-4). Although impressive progress has been made on both fronts, these approaches have inherent limitations. The study of large proteins is hampered by their extreme complexity, and it is difficult to synthesize small-molecule models capable of simultaneously binding diiron, oxygen, and various substrates. Recently, we and others have sought a molecular middle ground between these two extremes through the design of small proteins and peptid...

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“…There has been wide spread use of this simple design strategy as a method for rational design of b-hairpin folds (Dhanasekaran et al 1999;Mohanraja et al 2003). Imperiali and coworkers used this device beneficially for rational design of a small and synthetic protein called BBA (Struthers et al 1996) (Fig. 6).…”

Section: De Novo Design Of Hetero-chiral Proteinsmentioning

confidence: 99%

“…Ghadiris nanotube's and gramicidin-A perhaps best exemplify the prospect (Ghadiri et al 1994;Urry 1971;Wallace 2000). Likewise several reported hairpin peptides and mini-proteins directed or stabilized by one or more D chiral residues are examples of downsizing achieved by de novo design (Dhanasekaran et al 1999;Durani 2008;Struthers et al 1996). Possibly the first known heterochiral fold of complex sequence chirality was a hexapeptide reported by Fabiola et al (1997).…”

Section: De Novo Design Of Hetero-chiral Proteinsmentioning

confidence: 99%