Limits...
Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle.

Miller JP, Melicher MS, Schepartz A - J. Am. Chem. Soc. (2014)

Bottom Line: Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies.Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array.The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and ‡Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, Connecticut 06520-8107, United States.

ABSTRACT
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.

No MeSH data available.


(A) Ribbon diagram of the previously reportedZwit-YK β-peptidebundle structure determined by X-ray crystallography.9 The locations of the N- and C-termini of each strand areindicated by cyan and red coloring, respectively. Close-up of thepotential two-coordinate Cd2+ binding site formed at the(B) parallel and (C) perpendicular helix interface in a model of theZwit-YK-C octameric bundle. The perpendicular interface is rotated40 degrees for clarity. (D) Primary sequence of Zwit-YK-C monomer.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4210112&req=5

fig1: (A) Ribbon diagram of the previously reportedZwit-YK β-peptidebundle structure determined by X-ray crystallography.9 The locations of the N- and C-termini of each strand areindicated by cyan and red coloring, respectively. Close-up of thepotential two-coordinate Cd2+ binding site formed at the(B) parallel and (C) perpendicular helix interface in a model of theZwit-YK-C octameric bundle. The perpendicular interface is rotated40 degrees for clarity. (D) Primary sequence of Zwit-YK-C monomer.

Mentions: The design of Zwit YK-C was guidedby the previously reported structureof Zwit-YK (Figure 1A), a β3-peptide bundle possessing well-ordered tertiary structure and superiorthermal stability,9 and the large bodyof research on α-peptide assemblies that bind Cd(II).21 Examination of the Zwit-YK X-ray structure suggestedthat addition of a single β-homocysteine (β-Cys) residueto the Zwit-YK C-terminus would result in an octameric bundle containingtwo or four copies of two stereochemically and electrostatically distincttwo-coordinate metal binding sites (Figure 1B,C). One site is formed at the termini of two parallel helices andis repeated four times per bundle; the other is formed at the perpendicularinterface of two helices from opposite halves of the bundle, and isrepeated twice. Placing the β-Cys residue at the C-terminusalso avoids self-cleavage events that can potentially occur with internalβ-Cys residues. To evaluate this design, we prepared Zwit YK-C(Figure 1D) using standard solid phase methodsand characterized its affinity for various metal ions.


Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle.

Miller JP, Melicher MS, Schepartz A - J. Am. Chem. Soc. (2014)

(A) Ribbon diagram of the previously reportedZwit-YK β-peptidebundle structure determined by X-ray crystallography.9 The locations of the N- and C-termini of each strand areindicated by cyan and red coloring, respectively. Close-up of thepotential two-coordinate Cd2+ binding site formed at the(B) parallel and (C) perpendicular helix interface in a model of theZwit-YK-C octameric bundle. The perpendicular interface is rotated40 degrees for clarity. (D) Primary sequence of Zwit-YK-C monomer.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4210112&req=5

fig1: (A) Ribbon diagram of the previously reportedZwit-YK β-peptidebundle structure determined by X-ray crystallography.9 The locations of the N- and C-termini of each strand areindicated by cyan and red coloring, respectively. Close-up of thepotential two-coordinate Cd2+ binding site formed at the(B) parallel and (C) perpendicular helix interface in a model of theZwit-YK-C octameric bundle. The perpendicular interface is rotated40 degrees for clarity. (D) Primary sequence of Zwit-YK-C monomer.
Mentions: The design of Zwit YK-C was guidedby the previously reported structureof Zwit-YK (Figure 1A), a β3-peptide bundle possessing well-ordered tertiary structure and superiorthermal stability,9 and the large bodyof research on α-peptide assemblies that bind Cd(II).21 Examination of the Zwit-YK X-ray structure suggestedthat addition of a single β-homocysteine (β-Cys) residueto the Zwit-YK C-terminus would result in an octameric bundle containingtwo or four copies of two stereochemically and electrostatically distincttwo-coordinate metal binding sites (Figure 1B,C). One site is formed at the termini of two parallel helices andis repeated four times per bundle; the other is formed at the perpendicularinterface of two helices from opposite halves of the bundle, and isrepeated twice. Placing the β-Cys residue at the C-terminusalso avoids self-cleavage events that can potentially occur with internalβ-Cys residues. To evaluate this design, we prepared Zwit YK-C(Figure 1D) using standard solid phase methodsand characterized its affinity for various metal ions.

Bottom Line: Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies.Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array.The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and ‡Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, Connecticut 06520-8107, United States.

ABSTRACT
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.

No MeSH data available.