Analyzing phosphorylated proteins

• US 7,041,459 B2
• Filed: 05/21/2002
• Issued: 05/09/2006
• Est. Priority Date: 05/21/2001
• Status: Expired due to Fees

• Current Assignee: Virologic, Inc. (Laboratory Corporation Of America Holdings)
• Original Assignee: Monogram Biosciences, Inc. (Laboratory Corporation Of America Holdings)
• Inventors: Singh, Sharat, Zivin, Robert Allan
• Primary Examiner(s): Le, Long V.
• Assistant Examiner(s): Davis, Deborah A.
• Application Number:
  US10/153,312
• Publication Number:
  US 20030040016A1
• Time in Patent Office: 1,449 Days
• Field of Search: 435/6, 435/7.1, 435/7.72, 435/55, 435/56, 436/161, 436/808
• US Class Current: 435/7.1
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins
• CPC Class Codes: G01N 33/6842 Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• CPC Class Codes: Y10S 436/808 Automated or kit

Abstract

Methods, compositions and kits are disclosed for determining one or more target polypeptides in a sample where the target polypeptides have undergone phosphorylation. A mixture comprising the sample and a first reagent comprising a cleavage-inducing moiety and an IMAC resin for a binding site on a target polypeptide is subjected to conditions under which binding of respective binding moieties occurs. The binding site is the result of phosphorylation activity involving the target polypeptide. The method may be employed to determine the target polypeptide itself. In another embodiment the presence and/or amount of the target polypeptide is related to the presence and/or amount and/or activity of an agent such as an enzyme involved in phosphorylation of the target polypeptide. The interaction between the IMAC resin and the binding site brings the cleavage-inducing moiety into close proximity to a cleavable moiety, which is associated with the polypeptide and is susceptible to cleavage only when in proximity to the cleavage-inducing moiety. In this way, an electrophoretic tag for each of the polypeptides may be released. Released electrophoretic tags are separated and the presence and/or amount of the target polypeptides are determined based on the corresponding electrophoretic tags.

Claims

1. A method for determining the presence or absence of one or more target polypeptides in a sample suspected of containing the target polypeptides, the method comprising the steps of:

a)—

mixing the sample with a class-specific reagent and one or more electrophoretic probes, wherein the class-specific reagent comprises (i) a cleavage-inducing moiety having an effective proximity and (ii) an immobilized metal affinity chromatography (IMAC) resin that binds a phosphate group on the one or more target polypeptides, and wherein the one or more electrophoretic probes each comprises a binding moiety that specifically binds one of the target polypeptide(s) and one or more electrophoretic tags each attached thereto by a cleavable linkage, under conditions that permit the class-specific reagent and the one or more electrophoretic probes to bind to the one or more target polypeptides;

b)—

cleaving the cleavable linkage(s) of any of the one or more electrophoretic probes that are within the effective proximity of the cleavage-inducing moiety so that one or more electrophoretic tags are released; and

c)—

determining the presence or absence of the one or more target polypeptides based on the presence or absence of the released electrophoretic tag(s).

2. The method of claim 1 wherein said one or more target polypeptides is a plurality of target polypeptides.

3. The method of claim 2 wherein said cleavage-inducing moiety is a sensitizer that produces an active species.

4. The method of claim 3 wherein said sensitizer is a photosensitizer, said cleavable linkage is an oxidation-labile linkage, and said active species is selected from the group consisting of hydrogen peroxide, hydroxyl radical, superoxide anion, phenoxy radical, and singlet oxygen.

5. The method of claim 4 wherein said active species is singlet oxygen.

6. The method of claim 5 wherein said plurality of target polypeptides is in the range of from 2 to 100.

7. The method of claim 6 wherein said plurality of target polypeptides is in the range of from 5 to 50.

8. The method of claim 5 wherein said photosensitizer is selected from the group consisting of porphyrins, phthalocyanines, halogenated derivatives of a fluorescein dye, halogenated derivatives of a rhodamine dye, and naphthalocyanines.

9. The method of claim 5 wherein said cleavable linkage comprises an olefin, a thioether, a selenoether, a thiazole, an oxazole, or an imidazole.

10. The method of claim 5 wherein said electrophoretic probe is defined by the following formula:

T-(L-E)_k wherein;

T is a binding moiety specific for a target polypeptide, L is an oxidation-labile linkage, E is an electrophoretic tag, and k is an integer greater than or equal to 1.

11. The method of claim 10 wherein L is selected from the group consisting of olefins, thioethers, selenoethers, thiazoles, oxazoles, and imidazoles.

12. The method of claim 10 wherein E is a fluorescent, water-soluble organic compound having a molecular weight in the range of from about 150 to 2500 daltons.

13. The method of claim 10 wherein E has the form (M,D), wherein D is a fluorescent dye and wherein M is a mobility modifying moiety that is a bond or an organic molecule having up to 100 atoms other than hydrogen selected from the group consisting of carbon, oxygen, nitrogen, phosphorus, boron, and sulfur.

20. The method of claim 3 wherein said sensitizer is a photosensitizer.

21. The method of claim 3 wherein said cleavable linkage is an oxidation-labile linkage.

22. The method of claim 3 wherein said active species is selected from the group consisting of hydrogen peroxide, hydroxyl radical, superoxide anion, phenoxy radical, and singlet oxygen.

14. A kit for detecting the presence or absence of a plurality of target polypeptides in a sample, the kit comprising:

a class-specific reagent comprising a cleavage-inducing moiety and an IMAC resin specific for a phosphate group on the one or more target polypeptides; and

one or more electrophoretic probes each comprising a binding moiety specific for a target polypeptide and one of more electrophoretic tags attached by a cleavable linkage.

15. The kit of claim 14 wherein said cleavage-inducing moiety is a photosensitizer and said cleavable linkage is an oxidation-labile linkage.

16. The kit of claim 15 wherein said binding moieties of said one or more electrophoretic probes are antibody binding compositions.

17. The kit of claim 16 wherein said one or more electrophoretic probes are a plurality in the range of from 2 to 50.

18. The kit of claim 17 wherein each different electrophoretic probe is specific for a different target polypeptide.

19. The kit of claim 17 wherein each of said one or more electrophoretic probes is defined by the formula:

T-(L-E)_k wherein;

T is said binding moiety specific for a target polypeptide, L is said oxidation-labile linkage, E is an electrophoretic tag, and k is an integer greater than or equal to 1.