Folded state

Given that a sequence folds to a known native stmcture, what are the mechanisms in the transition from the unfolded confonnation to the folded state This is a kinetics problem, the solution of which requires elucidation of the pathways and transition states in the folding process. 

Many proteins frequendy require the assistance of other protein molecules called molecular chaperonins, for assuming the fine tertiary stmcture in vivo. In E. coli, two such chaperonin molecules bind transientiy to newly synthesized polypeptide monomers, preventing them from aggregating prematurely, until the polypeptides attain their folded state (10). 

JD Eloneycutt, D Thirumalai. The nature of folded states of globular proteins. Biopolymers 32 695-709, 1992. 

Figure 6.2 The molten globule state is an important intermediate in the folding pathway when a polypeptide chain converts from an unfolded to a folded state. The molten globule has most of the secondary structure of the native state but it is less compact and the proper packing interactions in the interior of the protein have not been formed.

Before protein molecules attain their native folded state they may expose hydrophobic patches to the solvent. Isolated purified proteins will aggregate during folding even at relatively low protein concentrations. Inside cells, where there are high concentrations of many different proteins, aggregation could therefore occur during the folding process. This is prevented by... 

The efficient uptake of precursor proteins depends on their presentation in a translocation competent state. This is maintained in vivo by the specific interaction with a highly conserved group of proteins, the heat-shock or stress related proteins (hps70s). These act as molecular chaperones and interact with the proteins to maintain them in a correctly folded state, a process which is ATP dependent. 

Folding What is the kinetic mechanism by which the folded state of the protein is reached ... 

We will limit ourselves to reviewing recent SAXS and SANS studies of putatively fully unfolded states formed at equilibrium. We direct readers interested in partially folded states (kinetic and equilibrium molten globules and their brethren) to a number of excellent recent articles and reviews (Kataoka and Goto, 1996 Kataoka et al., 1997 Uversky etal., 1998 Pollack et al., 1999 Doniach, 2001). Similarly, we will not discuss in detail the technical aspects of scattering studies or the precise interpretation of scattering profiles, but instead direct the reader to the appropriate resources (Glatter and Kratky, 1982 Doniach et al., 1995 Kataoka and Goto, 1996 Doniach, 2001). 

Stabilizing the folded state also benefits from optimizing hydrogenbonding interactions, with water providing donor and acceptor groups to polar side chains and main chain C=0 and N—H groups left exposed on the surface of the folded structure. Direct evidence for such... 

NMRrelaxation and diffusion experiments provide important insights into both the internal molecular dynamics and the overall hydrodynamic behavior of unfolded and partly folded states. Local variations in backbone dynamics are correlated with propensities for local compaction of the polypeptide chain that results in constriction of backbone motions (Eliezer et al., 1998, 2000). This can occur through formation of... 

Fig. 5. Partly folded states of apoMb formed in acid solution. The radius of gyration for each state is shown (data from Eliezer et at., 1995 Gast et al., 1994 Nishii et al., 1994), as is the population of secondary structure that develops during compaction (Barrick and Baldwin, 1993 Gilmanshin et al., 2001 data from Griko and Privalov, 1994). The helicity is expressed relative to that of holoMb.

Fig. 6. Schematic energy landscape for protein folding (folding funnel). The approximate regions of the energy landscape that correspond to the various partly folded states of apoMb are indicated on the right.

Polypeptide chains exist in an equilibrium between different conformations as a function of environment (solvent, other solutes, pH) and thermodynamic (temperature, pressure) conditions. If a polypeptide adopts a structurally ordered, stable conformation, one speaks of an equilibrium between a folded state, represented by the structured, densely populated conformer, and an unfolded state, represented by diverse, sparsely populated conformers. Although this equilibrium exists for polypeptide chains of any size, its thermodynamics and kinetics are typically different for oligopeptides and proteins. This can be broadly explained with reference to the different dimensionalities of the free-energy hypersurfaces of these two types of molecules. 

Historically, research on polypeptide structure, whether by experimental or computational means, has focused on the folded state only. This is because an array of methods exist for detailed investigation of the folded state of a polypeptide, and because the folded state is commonly the functionally active one. There are, however, two scenarios in which a full characterization of the unfolded state becomes as essential as the determination of the folded conformation. The first is in the study of... 

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