93 results about "Protein neddylation" patented technology

Methods for producing secreted receptor analogs and biologically active peptide dimers are disclosed. The methods for producing secreted receptor analogs and biologically active peptide dimers utilize a DNA sequence encoding a receptor analog or a peptide requiring dimerization for biological activity joined to a dimerizing protein. The receptor analog includes a ligand-binding domain. Polypeptides comprising essentially the extracellular domain of a human PDGF receptor fused to dimerizing proteins, the portion being capable of binding human PDGF or an isoform thereof, are also disclosed. The polypeptides may be used within methods for determining the presence of and for purifying human PDGF or isoforms thereof.

Methods are described for detecting protein-protein interactions, among two populations of proteins, each having a complexity of at least 1,000. For example, proteins are fused either to the DNA-binding domain of a transcriptional activator or to the activation domain of a transcriptional activator. Two yeast strains, of the opposite mating type and carrying one type each of the fusion proteins are mated together. Productive interactions between the two halves due to protein-protein interactions lead to the reconstitution of the transcriptional activator, which in turn leads to the activation of a reporter gene containing a binding site for the DNA-binding domain. This analysis can be carried out for two or more populations of proteins. The differences in the genes encoding the proteins involved in the protein-protein interactions are characterized, thus leading to the identification of specific protein-protein interactions, and the genes encoding the interacting proteins, relevant to a particular tissue, stage or disease. Furthermore, inhibitors that interfere with these protein-protein interactions are identified by their ability to inactivate a reporter gene. The screening for such inhibitors can be in a multiplexed format where a set of inhibitors will be screened against a library of interactors. Further, information-processing methods and systems are described. These methods and systems provide for identification of the genes coding for detected interacting proteins, for assembling a unified database of protein-protein interaction data, and for processing this unified database to obtain protein interaction domain and protein pathway information.

Disclosed herein are methods for detecting multiple compounds in a sample, involving: (a) contacting the sample with a mixture of binding reagents, the binding reagents being nucleic acid-protein fusions, each having (i) a protein portion which is known to specifically bind to one of the compounds and (ii) a nucleic acid portion which encodes the protein portion and which includes a unique identification tag; (b) allowing the protein portions of the binding reagents and the compounds to form complexes; (c) capturing the binding reagent-compound complexes; (d) amplifying the nucleic acid portions of the complexed binding reagents; and (e) detecting the unique identification tag of each of the amplified nucleic acids, thereby detecting the corresponding compounds in the sample. Also disclosed herein are kits for carrying out such methods.

Disclosed herein are molecules that include a deoxyribonucleic acid (DNA) covalently bonded to a protein and uses thereof.

A mutant hydrolase optionally fused to a protein of interest is provided. The mutant hydrolase is capable of forming a bond with a substrate for the corresponding nonmutant (wild-type) hydrolase which is more stable than the bond formed between the wild-type hydrolase and the substrate and has at least two amino acid substitutions relative to the wild-type hydrolase. Substrates for hydrolases comprising one or more functional groups are also provided, as well as methods of using the mutant hydrolase and the substrates of the invention. Also provided is a fusion protein capable of forming a stable bond with a substrate and cells which express the fusion protein.

A mutant hydrolase optionally fused to a protein of interest is provided. The mutant hydrolase is capable of forming a bond with a substrate for the corresponding nonmutant (wild-type) hydrolase which is more stable than the bond formed between the wild-type hydrolase and the substrate and has at least two amino acid substitutions relative to the wild-type hydrolase. Substrates for hydrolases comprising one or more functional groups are also provided, as well as methods of using the mutant hydrolase and the substrates of the invention. Also provided is a fusion protein capable of forming a stable bond with a substrate and cells which express the fusion protein.

Disclosed herein are methods for immobilizing a peptide or protein on a solid support. The method generally includes the following steps: (a) providing one or more templates attached to a solid support, wherein the one or more templates include (i) an RNA encoding a peptide and (ii) a peptide acceptor-linker linked to the RNA; and (b) subjecting the one or more templates to conditions that support translation and attachment of said peptide to said peptide acceptor, thereby synthesizing the one or more peptides on the solid support. Also disclosed herein are solid supports having at least one RNA-protein fusion component immobilized thereon, methods for generating protein arrays, and methods for screening molecules using these arrays.

Methods and compositions for the rapid and reversible destabilizing of specific proteins using cell-permeable, synthetic molecules are described. Stability-affecting proteins, e.g., derived from FKBP and DHFR proteins are fused to a protein of interest and the presence or absence of the ligand is used to modulate the stability of the fusion protein.

A mutant hydrolase optionally fused to a protein of interest is provided. The mutant hydrolase is capable of forming a bond with a substrate for the corresponding nonmutant (wild-type) hydrolase which is more stable than the bond formed between the wild-type hydrolase and the substrate and has at least two amino acid substitutions relative to the wild-type hydrolase. Substrates for hydrolases comprising one or more functional groups are also provided, as well as methods of using the mutant hydrolase and the substrates of the invention. Also provided is a fusion protein capable of forming a stable bond with a substrate and cells which express the fusion protein.

The present invention relates to the cloning, identification and characterization of the unique and entire genomic sequences encoding new porcine DC-SIGN and LSECtin proteins, including the novel nucleotide sequences of the full-length cDNA and genes of both pDC-SIGN gene and pLSECtin. Also provided are the nucleic acid molecules encoding newly discovered porcine ICAM-3 isoforms from porcine monocyte-derived dendritic cells and the use thereof. Specifically, the invention is drawn to an isolated nucleic acid molecule comprising a nucleotide sequence encoding one or more of porcine DC-SIGN, porcine ICAM-3, porcine LSECtin, a complement of the nucleotide sequence or a functional, defined portion of the nucleotide sequence or a protein fusion product linked to a protein that may be of porcine or human origin. Methods for isolating and cloning the new porcine genes and for using the new nucleotide sequences in improved methods for propagating viruses, particularly enveloped viruses, are additionally described herein. The invention further includes new transfected cells or cell lines that can stably express the porcine proteins, new antibodies and the like.

Biotinylation peptides are provided which can be fused with other peptides or proteins of interest using recombinant DNA techniques to provide efficient methods for biotinylating the resulting fusion proteins in vivo or in vitro.

Isolated nucleic acid molecules which encode proteins from Staphylococcus saprophyticus are described. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing nucleic acid molecules, and host cells into which the expression vectors have been introduced. The invention still further provides isolated proteins, mutated proteins, fusion proteins, antigenic peptides and methods for the treatment, prevention or detection of an S. saprophyticus-associated disease or disorder. Furthermore, the nucleic acid molecules and polypeptide molecules of the invention may be used for the identification of agents which modulate S. saprophyticus activity, e.g., a small molecules.

A method for forming a fusion protein that is expressed as a recombinant protein body-like assembly in host eukaryotic cells and organisms other than higher plants as host systems is disclosed. More particularly, peptides and proteins are fused to protein sequences that mediate the induction of recombinant protein body-like assembly (RPBLA) formation, are stably expressed and accumulated in these host cells after transformation with an appropriate vector. Methods for preparing the fusion protein are also disclosed.

The present invention relates to isolation and purification of proteins in aqueous two-phase systems (ATPS). Specifically the invention provides processes for partitioning of proteins of interest in ATPS by fusing said proteins to targeting proteins which have the ability of carrying said protein into one of the phases.

Peptides are produced as fusions with a suitable carrier protein. The carrier protein disclosed herein are adapted from the N-terminal domain of staphylococcus nuclease. This novel carrier protein acts to promote the over-expression of the peptide-protein fusion in the form of inclusion bodies, which minimizes in-cell proteolysis of desired peptides. The fusion protein is readily purified by conventional procedures or His-tag affinity chromatography when His-tag is inserted into the fusion protein. The target peptide is released from the purified fusion protein by a simple cleavage step and separated from the librated carrier protein by use of a reverse-phase HPLC process or by repeating the same affinity purification method. A particular advantage of the disclosed method, in addition to the obvious advantage of high yields, is its use for producing isotopically labeled peptides for NMR characterization of bioactive peptides and their interactions with target proteins.

Polyacrylamide-based methods of fabricating surface-bound peptide and protein arrays, the arrays themselves, and a method of using the arrays to detect biomolecules and to measure their concentration, binding affinity, and kinetics are described. Peptides, proteins, fusion proteins, protein complexes, nucleic acids, and the like, are labeled with an acrylic moiety and attached to acrylic-functionalized glass surfaces through a copolymerization with acrylic monomer. The specific attachment of glutathione S-transferase-green fluorescent protein (GST-GFP) fusion protein was more than 7-fold greater than the nonspecific attachment of non-acrylic labeled GST-GFP. Surface-attached GST-GFP (0.32 ng / mm2) was detectable by direct measurement of green fluorescent protein fluorescence and this lower detection limit was reduced to 0.080 ng / mm2 using indirect antibody-based detection. The polyacrylamide-based surface attachment strategy was also used to measure the kinetics of substrate phosphorylation by the kinase c-Src which is encoded by the Rous Sarcoma virus. The surface attachment strategy is applicable to the proteomics field and addresses denaturation and dehydration problems associated with protein microarray development.

The invention relates to fusion proteins comprising a stress protein fused with an engineered antibody or fragment that binds to mesothelin, or a stress protein fused with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment that binds to mesothelin. The invention also relates to fusion proteins comprising a stress protein fused with an antibody binding protein in combination with an engineered antibody or fragment that binds to mesothelin. The invention also relates to fusion proteins comprising an engineered antibody or fragment that binds specifically to mesothelin fused in frame with a biotin binding protein. The invention also provides fusion proteins comprising an engineered antibody or fragment, that binds to mesothelin, fused with an antibody binding protein. The invention also relates to methods of using fusion proteins of the invention to induce an immune response to mesothelin and to treat disease.

The present invention relates to a method for secreting and producing a target protein into cell culture broth. More particularly, the invention relates to a microorganism co-transformed with a recombinant expression vector containing E. coli outer membrane protein F (OmpF) and a recombinant expression vector containing a target protein to be secreted into cell culture broth, as well as a method of secreting and producing the target protein into cell culture broth by culturing the microorganism. According to the invention, the target protein can be secreted into cell culture broth in a pure form without fusion with other proteins so that the efficient isolation and purification of the target protein is possible.

A tyrosine kinase substrate is described. The tyrosine kinase substrate comprises a fusion protein which comprises a protein for labeling and a specific peptide fused with the protein for labeling. The specific peptide has an amino acid sequence including a glutamic acid residue and a tyrosine residue. The tyrosine kinase substrate is capable of being phosphorylated by a plurality of kinds of tyrosine kinases.