Folding of multidomain 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. 

Residual dipolar couplings have been used to refine and improve structures of proteins where there is an ill-defined hydrophobic core,37-110-"1 to identify protein folds in proteins of unknown structure,"2113 to properly orient the domains of multidomain proteins where there are few interdomain H- H NOEs,"4-"8 to orient the components of complexes where the orientation of those components is ill-defined,"9-122 and to obtain the conformation and orientation of ligands in the presence of large proteins.120121123... 

Itoh, K., Sasai, M. Cooperativity, connectivity, and folding pathways of multidomain proteins. Proc. Natl. Acad. Sci. U.S.A. 2008,105,13865-70. 

The growing family of known divalent cation-dependent proteases such as insulinase [51] and dibasic convertase [52], with the variant consensus HxxeH, also present interesting questions as to the possibility of a mirrored active site with or without conservation of the overall topology. Conversely, it is possible that entirely different proteins which have no zinc dependency and completely separate function may adopt the zinc endoprotease topology, simply because this fold provides a stable modular scaffold useful in the construction of multidomain proteins. Results of further structural studies are eagerly awaited. 

Longer cubic lattice heteropolymeric chains may also mimic some aspects of multidomain protein folding [86]. 

Kolb, V. A., Makeyev, E. V., and Spirin, A. S. (2000). Co-translational folding of a eukaryotic multidomain protein in a prokaryotic translation system. J. Biol. Chem. 275, 16597-16601. 

Usually, TS /1-solenoids represent only parts of larger multidomain proteins. Other trimeric motifs found in these proteins include a-helical coiled coils, TS /1-spirals, trimeric bundles of single-stranded /1-solenoids, and irregular globular structures. Some of these domains may be needed for correct folding of the TS /1-solenoid. 

Limited proteolysis. Flexible regions of proteins can sometimes be removed by digestion of the protein with different proteases. This technique is based on the techniques that were used to determine the core folded regions of proteins, most notably antibodies (Porter, 1973). Limited proteolysis can be used to remove flexible loops of proteins, or separate multidomain proteins into separate domains and has been used successfully in a number of instances (Noel et al., 1993 Sondek et al., 1996 Mazza et al., 2002). 

The termination module of surfactin synthetase is a 144 kDa four-domain enzyme responsible for the incorporation of the final amino acid (L-Leu) into the surfactin peptide and subsequent cyclization of the resulting product. The structure of the TE domain of this construct was previously solved. In the recently determined 2.6 A X-ray structure of the C-A-PCP-TE construct, the entire protein chain is evident in the electron density maps. " " The structural folds of the individual domains in this module are similar to structures of monomeric domains (Figure 13). The deviations observed in this multidomain structure include a slight difference in the hinge region of C domain subdomains and an orientation of the subdomains of the A domain that is not consistent with the open or closed conformations previously described. The A domain contains... 

Oligomeric states of similarly folded subunits can be very disparate in architecture through evolution and have implications in terms of functions as it has been well exemplified with the hemoglobin family (Royer et al. 2005). The gain of modularity expected by switching from a single domain to multidomains proteins and then to supramolecular assemblies, the fact that components of stable complexes are more conserved than transient ones as well as the fact that essential proteins tend to be subunit of complexes have been discussed from the point of view of evolution (Pereira-Leal et al. 2006 Bomberg-Bauer et al. 2005). 

Multidomain proteins are widespread in genomes. The tethering of domains may play a biophysical role in addition to enriching functional diversity. To explore the underlying biophysical principles of the complex folding processes of... 

Woutersen, S. and Hamm, P. Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution, /. Chem. Phys., 114, 2727, 2001. Zhou, R.H., Huang, X.H., Margulis, C.J., Margulis, C.J., and Berne, B.J. Hydrophobic collapse in multidomain protein folding. Science, 305,1605, 2004. 

The large therapeutic proteins, such as factor VIII, are often organized into distinct domains that play a critical role in their structure and function [29, 30]. The folding/unfolding behavior of these individual domains, and the interactions between them, may coordinate various functions in multidomain proteins. 

Type 1 copper proteins are the class of proteins for which cupredoxins were originally named. Type 1 copper proteins include both proteins with known electron transfer function (e.g., plastocyanin and rusticyanin), and proteins whose biological functions have not been determined conclusively (e.g., stellacyanin and plantacyanin). Although these proteins with unknown function cannot be called cupredoxins by the strict functional definition, they have been classified as cupredoxins because they share the same overall structural fold and metal-binding sites as cupredoxins. In addition, many multidomain proteins, such as laccase, ascorbate oxidase, and ceruloplasmin, contain multiple metal centers, one of which is a type 1 copper. Those cupredoxin centers are also included here. Finally, both the Cua center in cytochrome c oxidase (CcO) and nitrous oxide reductase (N2OR), and the red copper center in nitrocyanin will be discussed in this chapter because their metal centers are structurally related to the type 1 copper center and the protein domain that contains both centers share the same overall structural motif as those of cupredoxins. The Cua center also functions as an electron transfer agent. Like ferredoxins, which contain either dinuclear or tetranuclear iron-sulfur centers, cupredoxins may include either the mononuclear or the dinuclear copper center in their metal-binding sites. 

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