234 results about "TARP Protein" patented technology

The present invention relates to methods of conducting assays for enzymatic activity on microarrays useful for the large-scale study of protein function, screening assays, and high-throughput analysis of enzymatic reactions. The invention relates to methods of using protein chips to assay the presence, amount, activity and / or function of enzymes present in a protein sample on a protein chip. In particular, the methods of the invention relate to conducting enzymatic assays using a microarray wherein a protein and a substance are immobilized on the surface of a solid support and wherein the protein and the substance are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the substance and the protein. The invention also relates to microarrays that have an enzyme and a substrate immobilized on their surface wherein the enzyme and the substrate are in proximity to each other sufficient for the occurrence of an enzymatic reaction between the enzyme and the substrate.

The invention relates to a method for determining if a test compound, or a mix of compounds, modulates the interaction between two proteins of interest. The determination is made possible via the use of two recombinant molecules, one of which contains the first protein a cleavage site for a proteolytic molecules, and an activator of a gene. The second recombinant molecule includes the second protein and the proteolytic molecule. If the test compound binds to the first protein, a reaction is initiated whereby the activator is cleaved, and activates a reporter gene.

The present teachings provide methods and systems for the identification of proteins via peptide analysis. Some embodiments analyze proteins identified by analysis techniques such as mass spectrometry and build protein groups out of results. Groups can be formed by collecting like proteins and examining the group so as to identify if it is likely that only one form of a protein is present or, if there is enough evidence to support the presence of alternate forms. Various embodiments provide visual reports that can be interactive. These reports can allow a user to visualize relationships between proteins both intra- and inter-group. Methods are also introduced that can reduce the identification of false positives by taking into account a priori information.

In a method for producing a target substance by utilizing a microorganism, which comprises culturing the microorganism in a medium to produce and accumulate the target substance in the medium and collecting the target substance from the culture, there is used, as the microorganism, a mutant strain or recombinant strain of a microorganism in which maltose assimilation is controlled by an interaction between IIA.sup.Glc protein of glucose PTS and a protein involved in non-PTS uptake of maltose, and the interaction between the IIA.sup.Glc protein and the protein involved in non-PTS uptake of maltose is reduced or eliminated in the mutant strain or recombinant strain.

The invention relates to protein-protein interactions and methods for identifying interacting proteins and the amino acid sequence at the site of interaction. Using overlapping hexapeptides that encode for the entire amino acid sequences of the linker domains of human P-glycoprotein gene 1 and 3 (HP-gp1 and HP-gp3), a direct and specific binding between HP-gp1 and 3 linker domains and intracellular proteins was demonstrated. Three different stretches (617EKGIYFKLVTM627, (SEQ ID NO: 1) 658SRSSLIRKRSTRRSVRGSQA677 (SEQ ID NO: 2) and 694PVSFWRIMKLNLT706 (SEQ ID NO: 3) for HP-gp1 and 618LMKKEGVYFKLVNM631 (SEQ ID NO: 4), 648KAATRMAPNGWKSRLFRHSTQKNLKNS674 (SEQ ID NO: 5), and 695PVSFLKVLKLNKT707 (SEQ ID NO: 6) for HP-gp3) in linker domains bound to proteins with apparent molecular masses of ˜80 kDa, 57 kDa and 30 kDa. The binding of the 57 kDa protein was further characterized. Purification and partial N-terminal amino acid sequencing of the 57 kDa protein showed that it encodes the N-terminal amino acids of alpha and beta-tubulins. The method of the present invention was further validated with Annexin. The present invention thus demonstrates a novel concept whereby the interactions between two proteins are mediated by strings of few amino acids with high and repulsive binding energies, enabling the identification of high affinity binding sites between any interacting proteins.

The invention discloses a method of predicting interaction between chemical compounds and proteins based on random forest. The method includes: collecting information of target proteins which tend to interact with drug compounds to establish a target base; collecting the drug compounds for establishment of a training set and information of interaction relation between the drug compounds and the target proteins to establish a compound base; establishing the training set according to the information of the compound base and the target base; training by modified random forest algorithm on the basis of the training set to establish a predicting model; collecting the compounds for prediction and the information of the target proteins obtained in step (A) to establish a test set; predicting the test set on the basis of the predicting model; and (H), judging whether interaction between the compounds to be predicted and the target proteins exists or not according to the prediction result. Accuracy of predicting interaction between the compounds and the proteins by the method can be improved.

The present invention relates to a method for modulating the interaction between at least two proteins, wherein at least one of the two proteins is a functional cell-surface receptor and the other protein is the receptor ligand. The invention features a binding site of said functional cell-surface receptor on the receptor ligand and discloses a series of amino acid sequences, which are part of the structure of said binding site and / or involved in the interaction between the receptor and the ligand. Moreover, the present invention features methods for molecular design and screening of a candidate compound capable of modulating the interaction between the functional cell-surface receptor and receptor ligand through the described binding site, and provides a screening assay for identification of such a compound. The invention further describes an antibody capable of binding to the above binding site and / or to an epitope comprising an amino acid sequence essential for executing the receptor ligand interaction through said binding site. The invention also concerns a variety of uses of the disclosed methods, peptide sequences and antibodies. The invention in preferred embodiments concerns the binding site of the fibroblast growth factor receptor (FGFR) on FGFR ligands, compounds capable of modulating the receptor ligand interaction through sa d binding site, and antibody capable of recognition of said binding site.

A protein chip of a S-L-SP form wherein a substrate peptide (SP) is immobilized on a solid substrate (S) by the mediation of a linker protein (L). Such chip is usefully employed in a method for analyzing the interaction between a reactive protein and its substrate peptide involving the steps of: adding to the protein chip a reactive protein showing a specific interaction with the substrate protein immobilized on the protein chip; and detecting the interaction between the reactive protein and the substrate peptide. The use of such protein chip and methodology allows an increase in the reactivity between a peptide with low molecular weight and an enzyme with high molecular weight and between the peptide and a reactive antibody on the protein chip, so that the interaction between the peptide and the protein can be analyzed rapidly and massively.

The term “homology” or “homologous” means an amino acid similarity measured by the program, BLAST (Altschul et al (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25:33 89–3402), and expressed as —(% identity n / n). In measuring homology between a peptide and a protein of greater size, homology is measured only in the corresponding region; that is, the protein is regarded as only having the same general length as the peptide, allowing for gaps and insertions.

The present teachings provide methods and systems for the identification of proteins via peptide analysis. Some embodiments analyze proteins identified by analysis techniques such as mass spectrometry and build protein groups out of results. Groups can be formed by collecting like proteins and examining the group so as to identify if it is likely that only one form of a protein is present or, if there is enough evidence to support the presence of alternate forms. Various embodiments provide visual reports that can be interactive. These reports can allow a user to visualize relationships between proteins both intra- and inter-group. Methods are also introduced that can reduce the identification of false positives by taking into account a priori information.