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Engineered E2 For Increasing The Content Of Free LYS11-Linked Ubiquitin

a technology of free ubiquitin and lys11, which is applied in the direction of enzyme stabilisation, peptides, fusion with degradation motif, etc., can solve the problems of inefficient solution production of free ubiquitin multimers by ube2s, which assembles k-11 linked polyubiquitin, and poor efficiency of ubiquitin transfer to proteins on their own, so as to facilitate structural studies and increase efficiency. , the effect of high-level purification

Inactive Publication Date: 2014-10-09
MEDICAL RESEARCH COUNCIL
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The patent describes a new way to analyze and purify a specific protein called K11-linked chains, which are important for cell fate decisions. By modifying this protein, researchers have been able to produce a larger amount of the desired chains and better understand their structures. This method also allows for the removal of unwanted linkages, which can be useful for studying the biological effects of ubiquitination.

Problems solved by technology

In vitro these enzymes are very poor at transferring ubiquitin to proteins on their own, and probably require an E3 to aid this in vivo.
For instance, UBE2S, which assembles K-11 linked polyubiquitin, is inefficient at producing free ubiquitin multimers in solution, producing only small amounts of free ubiquitin dimers.

Method used

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  • Engineered E2 For Increasing The Content Of Free LYS11-Linked Ubiquitin
  • Engineered E2 For Increasing The Content Of Free LYS11-Linked Ubiquitin
  • Engineered E2 For Increasing The Content Of Free LYS11-Linked Ubiquitin

Examples

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example 1

Analysis of E2 Enzymes Involved in K11 Chain Formation

[0100]For the assembly of free K48- and K63-linked ubiquitin chains, specific E2 enzymes have been described, and the biology of these posttranslational modifications is now known in great detail. In order to study the elusive K11 linkage, Applicants analyzed the in vitro properties of two human E2 conjugating enzymes that have been associated with this chain type, namely UBE2C / UbcH10 (Jin et al., 2008) and UBE2S / E2-EPF (Baboshina & Haas, 1996). Applicants tested whether UBE2S and UBE2C would assemble unattached polyubiquitin chains in vitro in absence of an E3 ligase. Analytical assays were carried out in 30 μl reactions at 37° C. containing 250 nM ubiquitin-activating enzyme (E1), 2.8 μM (UBE2S) or 3.4 μM (UBE2C) ubiquitin conjugating enzyme (E2), 19.5 μM ubiquitin, 10 mM ATP, 40 mM Tris (pH 7.5), 10 mM MgCl2 and 0.6 mM OTT. After 1 h the reaction was stopped by addition of 10 μl 4×LDS sample buffer (Invitrogen), resolved by SD...

example 2

Generation of K11-Linked Ubiquitin Tetramers

[0105]In order to increase the yields of K11-linked dimers and to obtain longer polymers, Applicants reverted to protein engineering to create an UBE2S variant with increased capability to form free ubiquitin chains. Having established that the Lys-rich tail of UBE2S is polyubiquitinated by UBE2S in a cis reaction, Applicants replaced this tail (residues 196-222) with the ubiquitin binding ZnF-UBP domain of human USP5 / IsoT (residues 173-289) (Reyes-Turcu et al., 2006; FIG. 3a). This UBD has two advantageous features: it binds ubiquitin with nanomolar affinity, and interacts with the free C-terminal tail of ubiquitin leaving the Lys11 side chain accessible for chain elongation. The UBE2S-UBD fusion protein was significantly more efficient in producing ubiquitin dimers, trimers, and tetramers.

[0106]Ubiquitin tetramers were synthesized by incubating 250 nM E1 enzyme, 4.8 μM UBE2S-UBD, 2.9 mM ubiquitin, 400 nM AMSH, 10 mM ATP, 40 mM Tris (pH 7...

example 3

Structure of K11-Linked Polyubiquitin

[0109]Generation of K11-linked ubiquitin chains in large quantities allowed detailed structural analysis of this chain type.

[0110]Large-scale ubiquitin chain assembly was carried out in 1 ml reactions. Ubiquitin dimers were synthesized by incubating 250 nM E1 enzyme, 4.8 μM UBE2SΔC, 1.5 mM ubiquitin, 10 mM ATP, 40 mM Tris (pH 7.5), 10 mM MgCl2 and 0.6 mM DTT at 37° C. overnight. Subsequently, 50 mM DTT was added to the reaction before further dilution with 14 ml of 50 mM ammonium acetate (pH 4.5) to precipitate enzymes. The solution was filtered through a 0.2 μm syringe filter and K11-linked diubiquitin was purified by cation exchange using a MonoS column (GE Healthcare) and concentrated to 5 mg / ml. Crystals formed after 1 day from 3M NaCl and 0.1 M citric acid (pH 3.5). Before freezing in liquid nitrogen, crystals were soaked in mother liquor containing 15% ethylene glycol.

[0111]Diffraction data on crystals of K11-linked diubiquitin were collect...

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Abstract

The invention provides a chimeric E2 enzyme comprising a Ubc domain fused to a heterologous ubiquitin binding domain (UBD). The chimeric enzymes of the invention may be useful in producing elevated levels of free polyubiquitin.

Description

RELATED APPLICATIONS AND INCORPORATION BY REFERENCE[0001]This application is divisional of U.S. Ser. No. 13 / 670,594 filed Nov. 7, 2012, which is a continuation-in-part application of international patent application Serial No. PCT / GB2011 / 000704 filed 6 May 2011, which published as PCT Publication No. WO 2011 / 138593 on 10 Nov. 2011, which claims benefit of GB patent application Serial No. 1007704.8 filed 7 May 2010 and U.S. provisional patent application Ser. No. 61 / 333,145 filed 10 May 2010.[0002]The foregoing applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced in the appln cited documents, and all documents cited or referenced herein (“herein cited documents”), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by re...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12N9/96C12N9/48
CPCC12N9/48C12N9/96C07K2319/70C07K2319/95C12N9/485C12N9/93C12Y304/19012C12Y603/02019
Inventor KOMANDER, DAVIDBREMM, ANJA
Owner MEDICAL RESEARCH COUNCIL
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