17 results about "Protein methods" patented technology

Methods and systems for identifying a protein within a sample are provided herein. A panel of antibodies are acquired, none of which are specific for a single protein or family of proteins. Additionally, the binding properties of the antibodies in the panel are determined. Further, the protein is iteratively exposed to a panel of antibodies. Additionally, a set of antibodies which bind the protein are determined. The identity of the protein is determined using one or more deconvolution methods based on the known binding properties of the antibodies to match the set of antibodies to a sequence of a protein.

Methods and kits are provided for producing Griffithsin. The methods include providing a genetically modified microorganism comprising a gene encoding Griffithsin protein operably linked to an inducible promotor and growing the genetically modified microorganism under conditions that induce the promotor and cause expression of griffithisin. The Griffithsin is purified by releasing Griffithsin from the microorganism by cellular disruption, performing a precipitation step to remove contaminating protein and nucleic acids, and performing an anion exchange chromatography step.

Methods and compositions for detecting isoaspartate residues in polypeptides using mass spectrometry, and for distinguishing isoaspartate residues from aspartate and / or asparagine residues in a polypeptide using MS analysis. Polypeptides containing one or more isoaspartate residues, or suspected of containing one or more isoaspartate residues, are treated with L-isoaspartyl methyltransferase (PIMT), which is able to selectively modify isoaspartate and impart a mass change to the amino acid residue. The polypeptide is then analysed using mass spectrometry, where a mass change caused by the PIMT reaction is detected and characterized. Preferably, these methods are able to be performed without the use of liquid chromatography or other similar separation techniques prior to mass spectrometry analysis.

A fully automated pretreatment device for extracting selenium from water samples based on the acetic acid precipitation protein method, belonging to the field of testing equipment technology, includes a base and a material rack mechanism, a robotic arm, a transfer mechanism, a processing mechanism, and a filtration mechanism all connected to the base. The material rack mechanism is used to store sample tubes, a receiving container, and a filter element. The robotic arm is used to transfer sample tubes between the material rack mechanism and the transfer mechanism, and also to transfer the receiving container and filter element between the material rack mechanism and the filtration mechanism. The processing mechanism is used to process the solution in the sample tubes located on the transfer mechanism. The transfer mechanism is used to transfer the intermediate solution after processing by the processing mechanism to the filtration mechanism. The filtration mechanism is used to filter the intermediate solution through the filter element, and the receiving container is used to collect the filtered solution. This device can improve the degree of automation, reduce manual intervention, and improve processing efficiency, as well as the stability and accuracy of the results.

The present disclosure is concerned with proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids. In one embodiment, proteins are provided that selectively act on certain modified cytosines of target nucleic acids and converts them to thymine. Also provided are compositions and kits that include one or more of the proteins and methods for using one or more of the proteins.

Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for iteratively identifying candidate proteins within a sample of unknown proteins, the method comprising receiving information of binding measurements of each of a plurality of affinity reagent probes to the unknown proteins, each affinity reagent probe configured to selectively bind to one or more candidate proteins; comparing at least a portion of the information of binding measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein; and iteratively generating a probability that each of one or more candidate proteins is present in the sample based on the comparison of the information of binding measurements of the candidate proteins against the database comprising the plurality of protein sequences.

Methods and materials for making and using extracellular vesicles (EVs) engineered to include BMP2 or BMP2 in combination with BMP7, and cells that can be used to generate such EVs, are provided herein. For example, methods and materials for generating EVs that include BMP2 or BMP2 and BMP7, and methods and materials for using such EVs to induce bone formation, are provided. Methods and materials for making and using minicircle DNAs (mcDNAs) to overexpress BMP2 or BMP2 and BMP7 also are provided herein. For example, methods and materials for generating mcDNAs that encode BMP2 or BMP2 and BMP7, and methods and materials for using such mcDNAs to induce bone formation, are provided.

Methods for characterizing VP1 capsid proteins, VP2 capsid proteins, and VPS capsid proteins in adeno-associated virus (AAV) particles using liquid chromatography mass spectrometry and / or ultraviolet (UV)-visible spectroscopy are provided. The methods generally include the steps of: (a) subjecting AAV particles to liquid chromatography to denature and then separate the VP1 capsid proteins, the VP2 capsid proteins, and the VPS capsid proteins; and (b) subjecting the separated VP1 capsid proteins, VP2 capsid proteins, and VPS capsid proteins produced in step (a) to UV and mass spectrometry to determine the ratio and mass of the VP1 capsid proteins, the VP2 capsid proteins, and the VPS capsid proteins in the AAV particles. In another aspect, the disclosure provides an AAV composition comprising a post-translational modification. The disclosure also provides methods for characterizing the purity of an AAV composition using liquid chromatography mass spectrometry.

The present disclosure relates to modified proteins, methods, compositions and kits for mapping the methylation status of nucleic acids comprising 5-methylcytosine and 5-hydroxymethylcytosine. In some embodiments, the modified proteins have been altered to increase protein stability. In some embodiments, a protein selectively acts on certain modified cytosines of a target nucleic acid and includes one or more substitution mutations that enhance the protein's selectivity for certain modified cytosines, optionally enhance the stability of the protein, or optionally enhance both selectivity and stability. Also provided are compositions and kits comprising one or more of the proteins, as well as methods of using one or more of the proteins.

The present disclosure provides proteins, methods, and systems for targeting enzymes to specific subcellular locations to produce post-translational modifications on proteins. Specifically, kinases for phosphorylating proteins containing one or more sites susceptible to phosphorylation are disclosed, along with methods and systems for phosphorylating proteins of interest, such as proteins with nutritional and therapeutic uses. Recombinant host cells engineered to express a non-naturally occurring polypeptide comprising a heterologous serine / threonine kinase, wherein the heterologous serine / threonine kinase is anchored in an intracellular membrane, are disclosed herein.

Methods for producing proteins, cells for producing proteins, and methods for producing cells with improved protein production are provided. Methods of producing a selected protein, including expressing the selected protein in a cell expressing a Rheb (Ras homologue enriched in brain) protein having an activity to increase protein production in the cell, and secreting the selected protein from the cell, thereby producing the protein are provided.

The present disclosure provides for proteins, methods, systems for directing enzymes for generating post-translational modifications on proteins to a particular subcellular location. Specifically, kinases for phosphorylation of proteins containing one or more sites susceptible to phosphorylation are disclosed, also with methods and systems for phosphorylating proteins of interest, such as proteins having nutritional and therapeutic uses.

Methods and systems for identifying a protein within a sample are provided herein. A panel of antibodies are acquired, none of which are specific for a single protein or family of proteins. Additionally, the binding properties of the antibodies in the panel are determined. Further, the protein is iteratively exposed to a panel of antibodies. Additionally, a set of antibodies which bind the protein are determined. The identity of the protein is determined using one or more deconvolution methods based on the known binding properties of the antibodies to match the set of antibodies to a sequence of a protein.

Methods of predicting or designing a protein. The methods may include providing a protein that includes a target residue; centering a gridded box on a selected atom of the target residue; collecting local structural information adjacent the selected atom and the target residue; and determining the target residue of the protein based on the local structural information. The methods may include providing a nine-layer three-dimensional deep convolutional neural network (CNN) configured to accept as input data a gridded box comprising atomic coordinates and types adjacent a target residue; and analyzing the gridded box centered on the target residue with the three-dimensional deep convolutional neural network to determine the target residue.

Methods are disclosed for treating neurodegenerative disorders, such as ALS and FTD by using an effective amount of a type I protein arginine methyltransferase (Type I PRMT) inhibitor to decrease cellular toxicity caused by dipeptide repeat proteins (DRPs).

Methods and compositions for detecting isoaspartate residues in polypeptides using mass spectrometry, and for distinguishing isoaspartate residues from aspartate and / or asparagine residues in a polypeptide using MS analysis. Polypeptides containing one or more isoaspartate residues, or suspected of containing one or more isoaspartate residues, are treated with L-isoaspartyl methyltransferase (PIMT), which is able to selectively modify isoaspartate and impart a mass change to the amino acid residue. The polypeptide is then analysed using mass spectrometry, where a mass change caused by the PIMT reaction is detected and characterized. Preferably, these methods are able to be performed without the use of liquid chromatography or other similar separation techniques prior to mass spectrometry analysis.

Methods and kits are provided for amplifying and detecting αS proteins from samples, for example, from patients having Parkinson's Disease. For example, a method for determining a presence of a soluble, misfolded αS protein may include: contacting the sample with a monomeric, folded αS protein to form an incubation mixture; conducting an incubation cycle two or more times on the incubation mixture effective to form an amplified portion of misfolded αS protein; incubating the incubation mixture effective to cause misfolding and / or aggregation of at least a portion of the monomeric, folded αS protein in the presence of the soluble, misfolded αS protein; physically disrupting the incubation mixture effective to at least partly de-aggregate at least a portion of a misfolded αS aggregate present; and determining the presence of the soluble, misfolded αS protein in the sample by detecting at least a portion of the soluble, misfolded αS protein.