155 results about "Protein folding" patented technology

Biological macromolecules are synthesized in vitro under conditions and in a reaction composition wherein oxidative phosphorylation is activated and protein folding is improved.

Disclosed are methods of preventing, treating, or diagnosing in a subject a disorder in protein folding or aggregation, or amyloid formation, deposition, accumulation, or persistence consisting of administering to said subject a pharmaceutically effective amount of inositol stereoisomers, enantiomers or derivatives thereof.

The present invention relates to the fields of microbiology, molecular biology and protein biochemistry. More particularly, it relates to compositions and methods for analyzing and altering (e.g., enhancing or inhibiting) protein folding and solubility.

The invention relates generally to novel compositions and methods comprising one or more cyclohexanehexol and one or more NSAID. The compositions and methods provide beneficial effects in the treatment and prevention of diseases involving a disorder in protein folding and / or aggregation, and / or amyloid formation, deposition, accumulation, or persistence, in particular neurodegenerative diseases.

Disclosed are methods of preventing, treating, or diagnosing in a subject a disorder in protein folding or aggregation, or amyloid formation, deposition, accumulation, or persistence consisting of administering to said subject a pharmaceutically effective amount of inositol stereoisomers, enantiomers or derivatives thereof.

Analog processors such as quantum processors are employed to predict the native structures of proteins based on a primary structure of a protein. A target graph may be created of sufficient size to permit embedding of all possible native multi-dimensional topologies of the protein. At least one location in a target graph may be assigned to represent a respective amino acid forming the protein. An energy function is generated based assigned locations in the target graph. The energy function is mapped onto an analog processor, which is evolved from an initial state to a final state, the final state predicting a native structure of the protein.

The invention provides a method for the expression of exogenous DNA libraries in filamentous fungi. The fungi are capable of processing intron-containing eukaryotic genes, and also can carry out post-translational processing steps such as glyclosylation and protein folding. The invention provides for the use of fungi with altered morphology, which permits high-throughput screening and directed molecular evolution of expressed proteins. The same transformed fungi may be used to produce larger quantities of protein for isolation, characterization, and application testing, and may be suitable for commercial production of the protein as well.

Disclosed are methods and compositions that can be used to synthesize oligosaccharides; mutants of galactosyltransferases having altered donor and acceptor specificity; methods for increasing the immunogenicity of an antigen; and polypeptide stem regions that can be used to promote in vitro folding of polypeptides, such as the catalytic domain from a galactosyltransferase.

The invention provides compositions, methods and uses comprising a scyllo-inositol compound that provide beneficial effects in the treatment of a disorder and / or disease including a disorder in protein folding and / or aggregation, and / or amyloid formation, deposition, accumulation, or persistence.

An osmolyte composition comprising 4 M glycerol and 4M urea for stabilizing previously transient protein folding intermediates as long-lived stable forms. A method to search for other possible stabilizing osmolyte mixtures using a screening array is also provided. These additional osmolyte mixtures may complement or augment the successful 4M glycerol / 4 M urea mixture.

The invention relates to a protein folding parallel predicting method. The method includes the following steps: obtaining different protein structures through molecular dynamics simulation; setting different temperatures, and obtaining more protein structures with different conformations; partitioning the protein structures with different conformations through a conjugate cap molecule partitioning method, decomposing amino acids from proteins, and wearing a conjugate cap on each amino acid; calculating out the electrostatic potential of molecular fragments through quantum mechanics software to fit out the electric charge of each atom in each amino acid molecular fragment, and updating the electric charge of atoms in a molecule force field. To research protein folding, the scheme of considering a protein polarization effect and a copy interchange-based method are organically integrated, and then two difficult problems of atom interaction potential and a sampling technique in dynamics simulation can be overcome in order to achieve a good effect in protein folding simulation.

The invention concerns agents for the treatment of acute and chronic infections with human and animal pathogenic viruses which assemble along the cell membrane and are released through budding on the surface of the cell. Hereunto count especially causative agents of infectious diseases such as AIDS, hepatitis, hemorrhagic fever, SARS, smallpox, measles, polio or the flu. The subjects of the invention are agents that contain inhibitors of the protein folding as active components. Hereunto count inhibitors of cellular folding enzymes (the enzymatic chaperones) as well as substances that disturb the folding of proteins through chemical chaperones. The following substance classes and their derivates belong thereunto: Geldanamycin, Deoxyspergualin, 4-PBA or Herbimycin A. Due to these agents the highly organised processes of the assembly and the proteolytical maturation of virus structure proteins is disturbed. As a result the release and production of infectious decendent viruses is prevented.

A system and method for molecular dynamic simulation includes a database for storing data pertaining to at least one biomolecular system, a memory device for storing instructions for performing at least one algorithm having an electrostatic interaction calculating function and a multiple time step function, and subdividing forces on a basis of distance over which the forces act, and a processor for processing the data by executing the instructions in order to propagate the biomolecular system from a first set of coordinates to a second set of coordinates. The system and method significantly speed up the molecular dynamics simulation of biomolecular systems in which there are long-range and short-range electrostatic interactions and in which there are fast and slow motions, and make practicable the simulation of large protein solutions and thus, can be used to simulate protein folding and the binding of substrates to protein molecules.

The invention relates to a novel method for characterizing and multi-dimensionally representing the folding process of proteins (FIG. 9). Said method comprises, in a methodically novel combination, kinetically arranging the hydrodynamic size of the refolding and thus modified protein, associating the proteolytically fragmented intermediates on the basis of the bioinformatic detection patterns, classifying the folding pathway association of the intermediates, characterizing the folding sequences, and multi-dimensionally visualizing the characterized folding process in a computer-aided manner. Said method is characterized in that all intermediates modified during the refolding and thus structurally blocked are identified and digitalized according to the four individual characteristics of said intermediates, namely the hydrodynamic size, the formation time, the folding pathway association, and amount. Said novel method has many applications in the field of research of protein folding and proteopathy, protein engineering, antibody engineering, molecular biology, therapeutic medicine, biotechnology, biotechnological production of protein pharmaceuticals, protein taxonomy, and nanotechnology for developing and producing novel functional protein materials. According to the invention, many and varied products in the form of different assay kits, devices, software, and machines can be produced and used to carry out said method.

A system and method for molecular dynamic simulation includes a database for storing data pertaining to at least one biomolecular system, a memory device for storing instructions for performing at least one algorithm having an electrostatic interaction calculating function and a multiple time step function, and subdividing forces on a basis of distance over which the forces act, and a processor for processing the data by executing the instructions in order to propagate the biomolecular system from a first set of coordinates to a second set of coordinates. The system and method significantly speed up the molecular dynamics simulation of biomolecular systems in which there are long-range and short-range electrostatic interactions and in which there are fast and slow motions, and make practicable the simulation of large protein solutions and thus, can be used to simulate protein folding and the binding of substrates to protein molecules.

Methods, systems, algorithms and means for describing, analyzing and predicting protein folding motifs and other structures are provided. In one aspect, the Protein Folding Shape Code (PFSC) methods,systems, algorithms and means of the present invention apply generally to all of the categories of protein analysis and description, and are especially relevant to the geometric analyses and descriptions of proteins from their respective sequences or sequence portions. In a novel approach, the present inventions render analyses with respect to the alpha carbons of five-amino acid elements of a protein, utilizing available data to derive torsion angles and pitch distances, to thereby generate a series of overlapping analyses that can be expressed by a plurality of 27 vectors. Methods, systems and algorithms of the invention can be embodied in any computing device or portion thereof, and are adaptable to describe, analyze and predict the folding and other three-dimensional aspects of the structures of biomolecules such as nucleic acids, carbohydrates and glycoproteins. As yet another advantage, the present invention is adaptable as a tool for describing the conformations of many other organic molecules, and are thus especially suitable for use in the design of drugs, and the discovery and design of molecules which are to be adapted to interact with drugs.

The present invention relates to methods for treating endoplasmic reticulum (ER) stress-related conditions (e.g., cancer, protein folding / misfolding disease, diabetes mellitus) and for identifying compounds for treating ER stress-related conditions in a subject (e.g., a human). The invention also provides methods for diagnosing an ER stress-related condition in a subject and kits for the treatment of same.

The present invention relates to compositions and methods comprising peptides with high mutual affinity that, when attached to a protein, assist the protein to fold into a compact structure. By virtue of its stability and binding, this scaffold extends the activity of any contained protein sequence in the presence of cellular and other proteases. This compact structure may have other included functional sequences, which are superior to linear and less constrained peptides for library screening, building structure-biased peptide libraries, and targeting specific intracellular and extracellular compartments. The compositions of the present invention can be displayed on viral, archaeal, prokaryotic and eukaryotic cell surfaces for library screening, drug screening and display. The methods of the present invention are useful for in vivo screening of intracellular effector proteins that modulate signaling pathways, and for identification of interacting proteins in vitro. Therefore, the present invention can be used as a scaffold for gene therapy, for the isolation of new therapeutic drugs, and has potential utilization value for use as a therapeutic agent in physiological fluids.

The present invention provides an artificial chaperon useful for refolding the proteins having low voluntary folding ability and being difficult or unable to be a native form without a second (or assistant) of a molecular chaperon in a short time, and folding said proteins as an active form. The present invention relates to an artificial chaperon kit characterized in that the kit comprises cyclic saccharide cycloamylose and polyoxyethylenic detergent or cyclic saccharide cycloamylose and ionic detergent. The present invention also relates to a method for diluting the denaturant making the protein a denatured state by adding a specific detergent to a denatured protein, and preventing protein molecules from aggregation, thereafter adding cyclic saccharide cycloamylose, utilizing the inclusion ability thereof to strip detergent, accelerating the proper folding of protein into a correct higher-order structure with activity.

The present invention relates to the fields of microbiology, molecular biology and protein biochemistry. More particularly, it relates to compositions and methods for analyzing and altering (e.g., enhancing or inhibiting) protein folding and solubility (e.g., within periplasm). The present invention provides an engineered assay for protein folding and solubility in the E. coli periplasm based on co-translational translocation of a chimera comprising a protein of interest fused to TEM-I β-lactamase that is targeted for export via the signal recognition particle (SRP)-dependent pathway. Using an array of native and heterologous proteins, it is demonstrated that periplasmic folding behavior of proteins is intimately coupled to in vivo β-lactamase activity. As a result of this coupling, the reporter is useful for (1) facile discovery of extrinsic periplasmic factors that affect protein folding and solubility; and (2) genetic selection of solubility-enhanced proteins.

The invention relates to a method for performing fusion expression on a protein containing a disulfide bond, in particular to a method for performing fusion expression on a recombinant protein, in particular a eukaryotic recombinant protein of which the activity is closely related with the forming of the (intrachain and interchain) disulfide bond in an eukaryotic host cell. An exogenous recombinant protein is expressed in a pichia pastoris expression system by a method for fusing human protein disulphide isomerase (hPDI) or a mutant of the hPDI. The method is suitable for expressing a eukaryotic exogenous protein of which protein activity or protein folding (comprising forms of a monomer, a dimmer or a polymer) are resistant to the disulphide bond. The protein expressed by the mode can be secreted out of a cell easily, and is high in yield, products cannot be gathered on a large scale and can be captured and purified easily, and the obtained target protein is uniform in N tail end, and high in activity. The recombinant protein expressed by the method can be industrially produced on a large scale.

The invention relates to compositions, methods and uses comprising an epi-inositol compound that provides beneficial effects in the treatment of a disorder and / or disease including a disorder in protein folding and / or aggregation, and / or amyloid formation, deposition, accumulation, or persistence. In aspects of the invention, the epi-inositol compounds provide beneficial effects in the treatment of Alzheimer's disease, dementia, and mild cognitive impairment.

The invention relates to methods of enhancing normal melanocortin-4 receptor (MC4R) activity, and to enhancing activity of an MC4R having a mutation which affects protein folding and / or processing of the MC4R. The invention provides a method of treating an individual having a condition in which increased activity of an MC4R at the cell surface would be beneficial, for example in obesity, by administering an effective amount of a pharmacological chaperone for the MC4R. The invention provides MC4R pharmacological chaperones which enhance the activity of MC4R. The invention further provides a method of screening to identify pharmacological chaperones which enhance folding of an MC4R in the endoplasmic reticulum (ER), in order to enhance the activity of the MC4R at the cell surface.

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Internal polar and ionizable groups are essential for enzymatic catalysis, proton transport, redox reactions, and many other functional properties of proteins. To engineer novel enzymes or to modify the function of existing ones, and to build switches that can be used to modify the stability of proteins in response to changes in pH, it is necessary to introduce polar or ionizable groups or to modify the properties of existing ones. However, internal polar and ionizable groups usually destabilize proteins. The disclosure provides new methods that allow the introduction of polar and ionizable groups into the interior of proteins, as well as new methods for improving the accuracy of pKa of an internal amino acid of a protein, and methods for mapping the folding free energy landscape of a protein.

The invention relates to a novel substituted benzoyl urea compound and a preparation method and application thereof. The compound has the structure general formula disclosed in (I), wherein definitions of R1, R2, and R3 are described in the specification, and the compound can be used as a micromolecule inhibitor of Cyclophilin A (CypA); the CypA is a protein with the activity of Peptidyl-prolyl cis-trans isomerase (PPIase), and is related to the in vivo protein folding, assembly and transfer. The current research shows that the CrpA takes part in various physiology approaches, such as autoimmunity depression, HIV-1 invasion infection and the like. Therefore, the compound of the invention can become a novel immunosuppressive drug or anti-HIV-1 drug.

Many proteins, when produced recombinantly, suffer from improper processing, folding and lack normal solubility. Modified proteins, including those indicative of disease states, also can have such defects. The present invention is directed to methods of identifying proper and improper protein folding, aberrant processing and / or insolubility. The method relies on the use of two components: a specialized fusion protein and structural complementation. The fusion protein contains sequences from the protein of interest and one portion of a marker protein that, by itself, is not active. A host cell then provides the remainder of the marker protein that serves to "complement" the function of the fused marker protein such that their association restores activity, permitting detection.

The invention relates to systems and methods for producing proteins of interest. The invention employs genetically-engineered animal or plant cells that have modified protein folding or processing capacities. In one aspect, the invention features genetically-engineered cells comprising one or more recombinant expression cassettes which encode (1) a protein of interest and (2) a polypeptide that is functional in the unfolded protein response (UPR) pathway of the cells. Co-expression of the polypeptide significantly increases the yield of the protein of interest in the genetically-engineered cells. In one example, the genetically-engineered cells are animal cells, and the co-expressed polypeptide is a component or modulator of an XBP1- or ATF6-mediated UPR pathway.