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DNA & protein binding miniature proteins

a miniature protein and dna technology, applied in the field of polypeptide scaffolds, can solve the problems of difficult to envision a simple and general application of this truncation strategy

Inactive Publication Date: 2008-05-08
YALE UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The invention is about a modified polypeptide called avian pancreatic polypeptide, which can be used to inhibit or enhance interactions between other molecules and proteins. The modification involves substituting at least one amino acid residue on the polypeptide, which can be identified by analyzing the structure of the polypeptide. The modified polypeptide can be used in a phage-display library, and the invention also includes a nucleic acid encoding the modified polypeptide. The technical effect of the invention is the creation of a tool for studying interactions between proteins and other molecules.

Problems solved by technology

Despite this success, it is difficult to envision a simple and general application of this truncation strategy in the large number of cases where the alpha helical epitope is stabilized by residues scattered throughout the primary sequence.

Method used

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  • DNA & protein binding miniature proteins
  • DNA & protein binding miniature proteins
  • DNA & protein binding miniature proteins

Examples

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example 1

Synthesis of DNA-Binding Miniature Proteins

[0082] Polypeptides constituting miniature proteins were prepared using solid phase methodology and contain a carboxy-terminal amide and a free amino terminus unless otherwise indicated. High performance liquid chromatography (HPLC) was performed on either a Waters 600E Multisolvent Delivery System with a Waters 490E multiwavelength detector or a Rainin Dynamax SD-200 Solvent Delivery System with a Rainin Dynamax PDA-2 Diode Array Detector.

[0083] Solid phase peptide synthesis was performed on a Perseptive BioSearch 9600 peptide synthesizer. Standard research grade argon (Connecticut AirGas) was passed through an OxyClear oxygen scrubber before introduction to the synthesizer. HATU (O-(7-benzotrizol-1-yl)-1,1,3,3,-tetramethyl uronium hexafluorophosphate) was used as the activating reagent without addition of supplemental benzotrizole. Dimethylformamide, piperidine and methylene chloride (Baker) were fresh and stored under nitrogen. Anhydro...

example 2

Binding of Miniature Proteins to DNA

[0092] Miniature protein-binding to DNA was measured using a electrophoretic mobility shift assay performed in a Model SE600 Dual-Controller Vertical Slab Unit (Hoefer) using 14×16 cm gel plates. Temperature was controlled using a constant temperature bath. Reactions were performed in a binding buffer composed of 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.4 mM NaH2PO4 (pH 7.4), 1 mM EDTA, 0.1% NP-40, 0.4 mg / ml BSA (non-acetylated) and 5% glycerol. For experiments involving the bZIP peptide C / EBP152, the binding buffer was supplemented with 2 mM dithiothreitol. Serial peptide dilutions were performed as 1:1 dilutions with binding buffer. In general, 0.002 ml of gamma 32P-labeled, double-stranded DNA (CRE24, hsCRE24, C / EBP24 or hsCEBP24; final concentration ≦50 pM in binding buffer; final concentration ≦5 pM for peptides with Kappapp / peptideTn))−1] where n=1 for PPEBPSR and EBPSR and n=2 for C / EBP152. In these equations, theta=cpm in protein-DNA co...

example 3

Role of Hydrophobic Core in Miniature Protein-Binding to DNA

[0096] The contribution of hydrophobic core formation on PPBR4SR-hsCRE24 complex stability was examined utilizing UV circular dichroism experiments. Circular dichroism spectra were recorded in PBS on an Aviv-202 CD spectrometer and were background corrected but not smoothed. Wavelength scans were performed at 4° C. between 200 and 260 nm at 1 nm intervals with a recording time of five seconds at each interval. Thermal denaturation curves were measured at 222 nm between 4° C. and 98° C. with 2° C. steps and one minute equilibration at each temperature. Mean residue ellipticity and percent helicity were calculated from the value at 222 nm after background correction.

[0097] G27 lacked the polyproline helix and turn, whereas PPBR4-deltaSR contained D-tryptophan at position four and leucine at position thirty-one. Modeling studies suggested that these substitutions would disrupt core formation by kinking the polyproline or the...

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Abstract

The present invention provides a protein scaffold, such as an avian pancreatic polypeptide, that can be modified by substitution of two or more amino acid residues that are exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form.

Description

CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application is a continuation of U.S. patent application Ser. No. 09 / 840,085 filed Apr. 24, 2001; which application claims the benefit of U.S. Provisional Applications No. 60 / 199,408 filed Apr. 24, 2000; No. 60 / 240,566 filed Oct. 16, 2000; No. 60 / 265,099 filed Jan. 30, 2001; and No. 60 / 271,368 filed Feb. 23, 2001. These applications are incorporated herein by reference in their entirety.STATEMENT OF GOVERNMENT SUPPORT [0002] This invention was partially made with government support under National Institute of Health Grant 5-R01-GM59483 and 1-R01-GM65453-01.FIELD OF THE INVENTION [0003] The present invention relates to a polypeptide scaffold, such as an avian pancreatic polypeptide, that is modified by substitution of at least one amino acid residue that is exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form. The invention also relates to phage display libraries for such scaffolds. BACKGRO...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C07K14/00C07K7/00G01N33/50C07K14/465C12N7/00C12N15/09C12N15/10C12N15/12C12N15/62C12P21/02C12Q1/02C40B40/02G01N33/15G01N33/53
CPCC07K14/00C07K14/465C40B40/02C12N15/1037C12N15/62C07K2319/00
Inventor SHRADER, ALANNA SCHEPARTZCHIN, JASON W.K.ZUTSHI, REENARUTLEDGE, STACEY E.KEHLBECK MARTIN, JOANNE D.ZONDLO, NEAL J.
Owner YALE UNIV
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