Folding of conjugated proteins

Multidomain proteins may be viewed as conjugated proteins in which each domain may affect the folding dynamics and thermodynamic properties of its counterpart domain. Experimentally, the thermodynamics and kinetics of both isolated domains and conjugated constructs from several multidomain proteins were studied (a very detailed and fairly current report can be found in Reference [29]). A computational characterization of the mechanistic principles of the folding of multidomain proteins [33], utilizing native structure-based models, provides a reduced microscopic description of their folding, which in turn may enable the formulation of the forces involved in the interplay between neighboring domains. 

Small tfbiquitin-like modifier represents a family of evolutionary conserved proteins that are distantly related in amino-acid sequence to ubiquitin, but share the same structural folding with ubiquitin proteins. SUMO proteins are covalently conjugated to protein substrates by an isopeptide bond through their carboxyl termini. SUMO addition to lysine residues of target proteins, termed SUMOylation, mediates post-transla-tional modification and requires a set of enzymes that are distinct from those that act on ubiquitin. SUMOylation regulates the activity of a variety of tar get proteins including transcription factors. 

Add a quantity of adipic acid dihydrazide or carbohydrazide (Aldrich) to the protein solution to obtain at least a 10-fold molar excess over the amount of aldehyde functionality present. High molar ratios are necessary to avoid protein conjugation during the reaction process. If the concentration of aldehydes is unknown, the addition of 32mg adipic acid dihydrazide per ml of the protein solution to be modified should work well. 

Add a quantity of the crosslinker solution to the protein solution to obtain at least a 10-fold molar excess of the crosslinkers over the concentration of the protein. Studies should be done at several levels of crosslinker addition to determine the optimal conjugation conditions (i.e., 10-, 50-, 100-, and 200-fold excess). 

The sequence of amino acids in the long chain defines the primary structure of a protein. A secondary structure is determined when several residues, linked by hydrogen bonds, conform to a given combination (e.g., the a-helix, pleated sheet, and P-turns). Tertiary structure refers to the three-dimensional folded conformation of a protein. This is the biologically active conformation (crystal structure). A quaternary structure can result when two or more individual proteins assemble into two or more polypeptide chains. Conjugated proteins are complexes of proteins with other biomolecules, such as glycoproteins (sugar-proteins). 

More recently we have investigated whether the ubiquitin-proteosome system is perturbed in the heart of human DCM patients (Weekes et al, 2003). As in bovine DCM, expression of the enzyme UCH was elevated more than 8-fold at the protein level and elevated more than 5-fold at the mRNA level in human DCM. Moreover, this increased expression of UCH was shown by immuno-cytochemistry to be associated with the myocytes, which do not exhibit detectable staining in control hearts. Overall protein ubiquitination was increased 5-fold in DCM relative to control hearts. Using a selective affinity purification method we were able to demonstrate enhanced ubiquitination of a number of distinct proteins in DCM hearts. We have identified a number of these proteins by mass spectrometry. Interestingly many of these proteins were the same proteins previously found to be present at reduced abundance in DCM hearts (Corbett et al, 1998). This new evidence strengthens our hypothesis that inappropriate ubiquitin conjugation leads to proteolysis and depletion of certain proteins in the DCM heart and may contribute to loss of normal cellular function in the diseased heart. 

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