Described herein are compositions and methods for detecting the presence of ubiquitination in a sample. The compositions include synthetic peptides containing a high affinity ubiquitin binding domain and an additional peptide sequence that can be coupled to materials such as resins and dyes.

The present disclosure describes pan-SUMO trapping proteins and fusion proteins comprising the pan-SUMO trapping proteins that are stable and bind SUMO-modified proteins with high avidity. The proteins described herein can be used to detect the localization of SUMO-modified proteins cells. The proteins described herein can be used to identify biomarkers for diseases associated with oxidative stress. They can also be used to diagnose and monitor diseases associated with genotoxic and/or proteotoxic stress conditions.

The present disclosure provides methods for reducing the viscosity of a cell lysate or tissue lysate by: contacting the cell lysate or tissue lysate with a compressible and open-cell foam filter having a pore size from about 0.65 mm to about 1.22 mm, compressing the filter to recover the lysate absorbed in the filter, and collecting the filtered lysate; and also provides kits therefor.

Certain embodiments of the invention provide a method of quantifying ubiquitin-like modification in a test protein sample comprising: a) contacting the test protein sample with a compound of formula (I) to provide a first labeled test protein sample; b) contacting the first labeled test protein sample with a first enzyme, wherein the first enzyme cleaves the ubiquitin-like modification from all modified amino acid residues, to provide a second labeled test protein sample; c) contacting the second labeled test protein sample with a compound of formula (II) to provide a third labeled test protein sample; and d) measuring the molecular weight of the protein(s) in the third labeled test protein sample to quantify the ubiquitin-like modification in the test protein sample, wherein the compound of formula I is isotopically labeled; the compound of formula II is isotopically labeled; or the compound of formula I and the compound of formula II are differentially isotopically labeled.

An object of the present invention is to provide a method for efficiently identifying a polyubiquitinated substrate which is generally not easily identified. The method for identifying a polyubiquitinated substrate includes (1) a step of expressing a trypsin-resistant polyubiquitin chain-binding protein and a ubiquitin ligase in a cell, (2) a step of isolating a complex that contains the trypsin-resistant polyubiquitin chain-binding protein from the cell having undergone the step (1), (3) a step of subjecting the complex isolated by the step (2) to trypsin digestion, and (4) a step of identifying a peptide that has a ubiquitination site from a digested material obtained by the step (3).

Disclosed herein are methods and compositions for inhibiting neddylation using Glycyl-tRNA synthase (GlyRS) inhibitors. Also disclosed are related compositions and methods for treating diseases such as cancer.

Anti-K63-linked polyubiquitin monoclonal antibodies, and methods for using the antibodies, are provided.

The free thiol group present in free cysteines in recombinant therapeutic antibodies are reactive to process components and generates product variants during early stages of biosimilar development. Free thiol group present on the structural motifs, especially in the complementary determining regions (CDR), support maximal antigen binding capability. Product variants associated with these free thiol groups are detrimental for safety and efficacy of these therapeutic antibodies. Methods to identify and characterize various thiol variants an antibody composition is provided and an anti-IL-17A IgG1 composition having these thiol variants are described.

The invention provides antibodies having greater avidity for a mixed-topology polyubiquitin than a single-topology polyubiquitin and multispecific anti-polyubiquitin antibodies, and methods of using the same.

Disclosed is a recombinant protein composed by the fusion of Glutathione S-transferase (GST), or an esa-histidine peptide (poly-His), or Maltose Binding Protein (MBP), to the Carboxyl-terminus end of the human KHNYN protein, containing residues 597-678 or a region including at least the amino acidic region 630-678. Also disclosed is a second recombinant protein where the Carboxyl-terminus end of the human KHNYN protein, containing residues 627-678 is genetically fused in a tandem construct to the Carboxyl-terminus end of KHNYN including residues 597-678. The tandem construct is N-terminally tagged with Glutathione S-transferase (GST), or an esa-histidine peptide (poly-His), or Maltose Binding Protein (MBP). The potential use of these Neddylation sensors also called Neddylation probes to isolate mono-, poly-neddylated targets as well as substrates modified by the addition of ubiquitin-NEDD8 mixed chains is considered.