Molten globule intermediates and protein folding

How reverse turns may mediate the formation of helical segments in proteins: an x-ray model

The three-dimensional structure of a protein is the assembly of different secondary structural elements, such as alpha-helices, beta-pleated sheets, and beta-turns. Although the conformation of hundreds of proteins has been elaborated in the solid state, only a vague understanding of the mechanism of their conformational folding is known. One facet of this topic is the conformational interconversion of one or more beta-turns to a helical structure (and vice versa), which may also be related to the formation of helix-turn-helix motifs often observed in globular proteins. Based on a comprehensive structural analysis of proteins, Sundaralingam and Sekharudu [Sundaralingam, M. & Sekharudu, Y. C. (1989) Science 244, 1333-1337] previously suggested that "structure-water" molecules in proteins may mediate such a conformational change. An x-ray crystal structure determination of t-butoxycarbonyl (Boc)-Val-Ser-NHCH3 reveals (i) an ideal type I beta-turn backbone conformation and (ii) a hydrogen-bond network more typical of an alpha-helix than a beta-turn conformation. The molecular packing of this simple beta-turn model reported here provides a plausible and simple alternative of how a beta-turn-like conformation may serve as a conformational template for helical-structure formation (and vice versa) during the folding procedure.

Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state

In the study of protein folding, much attention has focused on the characterization of folding intermediates. We report here molecular dynamics simulations in which the initial stages of the thermal denaturation of hen egg white lysozyme in aqueous solution are examined in detail. It is found that lysozyme unfolds in a two-stage process with the initial formation a quasi-stable state in which significant rearrangement of the secondary structure takes place. No evidence for distinct folding domains was found. The simulations suggest that the formation of well-defined secondary structure occurs after the initial collapse of the peptide chain and thus tend against the framework model of protein folding.

The role of retinal in the thermal stability of the purple membrane

Differential scanning calorimetry demonstrates that the bleached form of the purple membrane does not possess any measurable thermal transition in water, up to 105 degrees C, whereas in 0.1 M phosphate pH 7.5 it shows a transition at about 82 degrees C, with an enthalpy of 110 kJ/mol. In the latter medium, the native membrane shows the main transition at 97 degrees C, with an enthalpy of 390 kJ/mol. The reduced form of the purple membrane shows two small transitions in water, as well as in 0.1 M phosphate, which do not seem to be related to the main thermal transition of the native membrane. Fourier-transform infrared spectra in D2O show that the two modified samples, as well as the native one, undergo similar secondary structural changes upon thermal denaturation. These changes appear to extend through a wide temperature range for both modified forms, particularly for the bleached one. The results suggest that the main thermal transition in the purple membrane is due to a cooperative conformational change involving the disruption of the network of electrostatic and hydrogen-bonding interactions which originate from the protonated Schiff base. In the two modified membranes, these conformational changes appear to proceed smoothly through a rather low or non-cooperative process. The thermal behaviour of the bleached membrane in water resembles that of the molten globule state described for several globular proteins.

Collapsed intermediates in the reconstitution of dimeric aspartate aminotransferase from Escherichia coli

Aspartate aminotransferase from Escherichia coli, which had been denatured by guanidinium chloride, refolded and reassembled to active dimers in two distinct phases. The unfolded monomer U collapsed within 20 s to an intermediate I* that was inactive, fluoresced more strongly than, but had the same peptide CD signal as the native dimer. The formation of crosslinkable dimers, as well as the recovery of enzyme activity, occurred with a biphasic progress curve which was independent of protein concentration. The half-lives of the two phases were 100 s and 2000 s. The data are consistent with a three-step mechanism, in which the overall rate of reassembly is determined by an isomerization of I* to the assembly-competent monomer M. The latter does not accumulate because it dimerizes rapidly to the active enzyme (D). Reassembly of the enzyme from the compact intermediate M*, which is stable at 1.0 M guanidinium chloride, also proceeded in a rapid and a slow phase. Moreover, the formation of M* from the unfolded state was rapid, whereas its refolding to the native dimer was slow. Both the transient intermediate I* and the equilibrium intermediate M* qualify as 'collapsed intermediate' or 'molten globule' states.

On the interpretation of biochemical data by molecular dynamics computer simulation

The application of computer simulation to molecular systems of biochemical interest is reviewed. It is shown that computer simulation is a tool complementary to experimental methods, which can be used to access atomic details inaccessible to experimental probes. Examples are given in which computer simulation augments the experimental information by providing an atomic picture of high resolution with respect to space, energy or time. The usefulness of a computer simulation largely depends on its quality. The most important factors that limit the accuracy of simulated results are discussed. The accuracy of different simulation studies can differ by orders of magnitude. The accuracy will depend on the type of biomolecular system and process studied. It will also depend on the choice of force field, the simulation set-up and the protocol that is used. A list of quality-determining factors is given, which may be useful when interpreting simulation studies appearing in the literature.

Effects of glycosylation on the folding and stability of human, recombinant and cleaved alpha 1-antitrypsin

The equilibrium unfolding transitions for the human M form of alpha 1-antitrypsin have been determined using a number of techniques reflecting changes in tryptophan fluorescence lifetime and quenching, exposure of tryptophan to solvent, secondary structure and the Stokes' radius of the protein. The denaturation curves are more complex than is usual for globular proteins and indicate the presence of multiple equilibrium intermediates in the presence of denaturant. This is in marked contrast to the more co-operative transition of the cleaved inhibitor. In addition, a recombinant non-glycosylated alpha 1-antitrypsin has been shown to have a closely similar conformation to the human M protein and to exhibit very similar reversible unfolding transitions, and hence similar stability and co-operativity. Differences in tryptophan environment are reflected in the dequenching of tryptophan fluorescence and reduced asymmetry in the near ultraviolet circular dichroism of the non-glycosylated protein, suggesting direct interaction of glycosyl residues with a tryptophan. Both the M type and the recombinant protein exhibit similar patterns of folding, with rapid collapse to a compact intermediate reminiscent of the widely observed molten globule state that folds more slowly to the native protein. The papain-cleaved M form also folds through a similar compact state in the absence of the C-terminal peptide that results from cleavage. It is concluded that part of the C-terminal 36 residue peptide interacts strongly with the main body of the protein in the folded inhibitor. This interaction will also be important during early stages of folding of the intact protein to direct the folding pathway. The lack of glycosylation leads to an increase in aggregation of the recombinant protein upon refolding, especially after extended denaturation times. The more rapid turnover of the recombinant protein in vivo is shown not to be due to a lower thermodynamic stability, but may be associated with a lower kinetic stability arising from the increased tendency to aggregation.

Calorimetric determination of the energetics of the molten globule intermediate in protein folding: apo-alpha-lactalbumin

High-sensitivity differential scanning calorimetry has been used to characterize the energetics of the molten globule state of apo-alpha-lactalbumin. This characterization has been possible by performing temperature scans at different guanidine hydrochloride (GuHCl) concentrations in order to experimentally define the temperature-GuHCl stability surface of the protein. Multidimensional analysis of the heat capacity surface has allowed simultaneous resolution of the energetics of the unfolded and molten globule states. These experiments indicate that the intrinsic enthalpy difference (i.e., excluding additional contributions such as those arising from differential GuHCl binding) between the unfolded and native states is 31.8 kcal/mol at 25 degrees C whereas that of the molten globule and native states is only 7.7 kcal/mol. At the same temperature, the entropy changes are 99.2 and 23.7 cal/K.mol and the heat capacity changes are 1821 and 326 cal/K.mol, respectively. Analysis of the thermodynamic data indicates that in passing from the native to the molten globule state only approximately 19% of the hydrogen bonds are broken. In addition, the magnitude of delta Cp for the molten globule suggests that water does not largely penetrate into the interior of the molten globule, implying that significant hydrophobic interactions are still present in this state. These parameters provide precise energetic constraints to the allowed structural conformations of the molten globule.