One aspect of the present invention describes materials and methods of quantitatively measuring the density or percent occupancy of DNA binding proteins such as histones, histone variants, histone post translational modifications and transcription factors in chromatin at given DNA loci. One embodiment measures a factor's average quantity at specific gene loci, and controls for a number of pitfalls concerning antibody quality and handling issues. Other embodiments include calibrating and quantifying chromatin immunoprecipitation assays, assessing an affinity reagent specificity, as well as required reagents and their formulation in kits. Another embodiment allows for the diagnosis of a condition or disease by measuring the density of a histone modification at a genomic locus.

Methods for in situ detecting proximity of two targets of interest featuring an antibody conjugated with a cleavable bridge component having a detectable moiety and an antibody conjugated with a non-cleavable bridge component. The bridge components each have a chemical ligation group adapted to form a covalent bond under particular conditions and when the targets are in close proximity. Following covalent bond formation, the cleavable bridge component can be cleaved from the antibody, effectively transferring the detectable moiety to the non-cleavable bridge component. Detection of the detectable moiety is indicative of the targets being in close proximity. The methods are compatible with both chromogenic and fluorogenic detection systems. The methods may be used to perform assays wherein one or more than one proximity event is detected on the same slide.

Examination of a test sample to determine the presence or quantity of succination of proteins is described. Examination can be via protein hydrolysis in total succination determination or via enzymatic digestion of isolated proteins and determination of the presence or quantity of modified peptides. The methods can be utilized for determination of excessive succination of lymph system proteins, which can be utilized in prevention or early detection of lymphopenia. Methods can be utilized for test samples of subjects under treatment with dimethyl fumarate suffering from multiple sclerosis. Methods can be utilized as a determination that treatment of the subject with DMF should be slowed or stopped.

The present invention provides a method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value K for said protein-modifying enzyme on the basis of the number of modified peptides in a sample that are substrates of said protein modifying enzyme, the intensity of the modified peptides, each modified peptide in the sample that is a substrate of said protein modifying enzyme, the total number of modified peptides in the sample, the intensity of the modified peptides and all of the modified peptides in the sample. A method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value SC for said protein-modifying enzyme on the basis of a reduction in proliferation using an inhibitor at an inhibitor concentration at which proliferation is measured and the in vitro IC50i of the inhibitor against a primary target is also provided. The invention further provides methods of identifying inhibitors with which to treat a patient, methods of treatment, a computer readable medium, a computer program product and devices for carrying out the methods.

The invention provides methods and formulations comprising a protein comprising solvent accessible amino acid residues susceptible to oxidation wherein N-acetyl tryptophan (NAT) is used to prevent oxidation of the protein. The invention also provides methods for making such formulations and methods of using such formulations. Methods to measure degradation of NAT in protein formulations are also provided.

One aspect of the present invention describes materials and methods of quantitatively measuring the density or percent occupancy of DNA binding proteins such as histones, histone variants, histone post translational modifications and transcription factors in chromatin at given DNA loci. One embodiment measures a factor's average quantity at specific gene loci, and controls for a number of pitfalls concerning antibody quality and handling issues. Other embodiments include calibrating and quantifying chromatin immunoprecipitation assays, assessing an affinity reagent specificity, as well as required reagents and their formulation in kits. Another embodiment allows for the diagnosis of a condition or disease by measuring the DNA density of a histone modification at a genomic locus.

The present invention relates to methods for detecting sulfenylation within thiol groups in proteins, metabolites, or materials. Protein sulfenylation (Cys-SOH) describes the reversible post-translational modification of protein thiols by hydrogen peroxide, and plays a central role in oxidative signaling (see, e.g., Paulsen, C. E. & Carroll, K. S. 2013 Chemical Reviews 113, 4633-679). Growth factor stimulation activates NADPH oxidase enzymes, releasing a local burst of hydrogen peroxide, which transiently oxidizes the nuclcophilic cysteine of protein phosphatases and other proximal redox active thiols (see, e.g., Paulsen, C. E. et al., 2012 Nature Chemical Biology 8, 57-64). In addition to masking functional cysteine's, sulfenylation is also a critical intermediate towards irreversible cysteine oxidation.

The present disclosure relates to the field of molecular biology and more specifically to methods for detecting anti-carbamylated protein (anti-CarP) antibodies in the serum of rheumatoid arthritis (RA) patients.

This disclosure provides methods, systems, and compositions of matter for studying solvent accessibility and three-dimensional structure of biological molecules. A plasma can be used to generate marker radicals, which can interact with a biological molecule and mark the solvent-accessible portions of the biological molecule.

Methods and compositions related to lipoproteins reactions are provided. Particularly, quantitation of lipoprotein subgroup particle numbers may be used to detect lipoprotein's response to oxidation conditions and incubation conditions. In further aspects, ultracentrifugation may be improved to analyze the lipoprotein profiles. Embodiments are directed to methods for generating a oxidation susceptibility measure for serum lipoproteins. In certain aspects a first portion of a serum sample is used to generate a base lipid particle profile (LPP) and a second portion of the serum sample is used to generate an oxidized lipid particle profile.