Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding

Structural perturbation has been extensively used in protein folding studies because it yields valuable conformational information regarding the folding process. Here we have used N-terminal truncation on a cross-linked variant of the GCN4-p1 leucine zipper, aiming to develop a better understanding of the folding mechanism of the coiled-coil motif. Our results indicate that removing the first heptad repeat in this cross-linked GCN4-p1 coiled coil significantly decreases the folding free energy barrier and results in a maximum folding rate of (2.0 +/- 0.3 micros)(-1), which is approximately 50 times faster than that of the full-length protein. Therefore, these results suggest that a set of native or nativelike tertiary interactions, distributed throughout the entire sequence, collectively stabilize the folding transition state of the GCN4-p1 coiled coil. While stable subdomains or triggering sequences have been shown to be critical to the stability of GCN4 coiled coils, our results suggest that the folding of such a subdomain does not seem to dictate the overall folding kinetics.     

Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding.

The folding of coiled coil peptides has traditionally been interpreted in terms of native dimer and unfolded monomers. Calculations using AGADIR and experimental studies of fragments suggest that the monomers of the coiled coil peptide, GCN4-p1, contain significant residual helical structure. A simple model based on diffusion-collision theory predicts not only the measured folding rate within an order of magnitude, but also predicts remarkably well the effect of alanine to glyXcine mutations. We suggest that intrinsic helix stability is a major determinant of the folding rate of the GCN4 coiled coil.     

T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1

Partially folded intermediates have been frequently observed in equilibrium and kinetic protein folding studies. However, folding intermediates that exist at the native side of the rate-limiting step are rather difficult to study because they often evade detection by conventional folding kinetic methods. Here, we demonstrated that a laser-induced temperature-jump method can potentially be used to identify the existence of such post-transition or hidden intermediates. Specifically, we studied two cross-linked variants of GCN4-p1 coiled-coil. The GCN4 leucine zipper has been studied extensively and most of these studies have regarded it as a two-state folder. Our static circular dichroism and infrared data also indicate that the thermal unfolding of these two monomeric coiled-coils can be adequately described by an apparent two-state model. However, their temperature-jump-induced relaxation kinetics exhibit non-monoexponential behavior, dependent upon sequence and temperature. Taken together, our results support a folding mechanism wherein at least one folding intermediate populates behind the main rate-limiting step.     

D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding

We have exploited a procedure to identify when hydrogen bonds (H-bonds) form under two-state folding conditions using equilibrium and kinetic deuterium/hydrogen amide isotope effects. Deuteration decreases the stability of equine cytochrome c and the dimeric and crosslinked versions of the GCN4-p1 coiled coil by approximately 0. 5 kcal mol-1. For all three systems, the decrease in equilibrium stability is reflected by a decrease in refolding rates and a near equivalent increase in unfolding rates. This apportionment indicates that approximately 50% of the native H-bonds are formed in the transition state of these helical proteins. In contrast, an alpha/beta protein, mammalian ubiquitin, exhibits a small isotope effect only on unfolding rates, suggesting its folding pathway may be different. These four proteins recapitulate the general trend that approximately 50% of the surface buried in the native state is buried in the transition state, leading to the hypothesis that H-bond formation in the transition state is cooperative, with alpha-helical proteins forming a number of H-bonds proportional to the amount of surface buried in the transition state.     

An intrahelical salt bridge within the trigger site stabilizes the GCN4 leucine zipper

We previously reported that a helical trigger segment within the GCN4 leucine zipper monomer is indispensable for the formation of its parallel two-stranded coiled coil. Here, we demonstrate that the intrinsic secondary structure of the trigger site is largely stabilized by an intrahelical salt bridge. Removal of this surface salt bridge by a single amino acid mutation induced only minor changes in the backbone structure of the GCN4 leucine zipper dimer as verified by nuclear magnetic resonance. The mutation, however, substantially destabilized the dimeric structure. These findings support the proposed hierarchic folding mechanism of the GCN4 coiled coil in which local helix formation within the trigger segment precedes dimerization.     

Effect of pressure on the secondary structure of coiled coil peptide GCN4-p1

It has recently been demonstrated that pressure induces folding of the α-helix of an alanine-based peptide (AK20), which is a monomer in water (Imamura and Kato, Proteins 2009;76:911–918). The present study focused on a coiled coil peptide GCN4-p1, the α-helices of which associate via a hydrophobic core, to examine whether the pressure stability of the α-helices depends on the hydrophobic core. Fourier transform infrared spectroscopy was used to investigate the effect of pressure on the secondary structures of GCN4-p1. The infrared spectra of GCN4-p1 shows the two amide I' peaks at ∼ 1650 and ∼ 1630 cm^− 1 stemming from the solvent-inaccessible α-helix and the solvent-accessible α-helix, respectively. The intensities of both the peaks increase with increasing pressure, whereas they decrease with increasing temperature. This indicates that pressure induces both the α-helices of GCN4-p1 to fold. The present result suggests that the positive volume change upon unfolding of an α-helix is a common characteristic of peptides. The pressure-induced stabilization of the α-helices is discussed in comparison with the pressure denaturation of proteins.     

Preformed secondary structure drives the association reaction of GCN4-p1, a model coiled-coil system

The structure of the transition state for the rate-limiting step in the folding and association of the homodimeric coiled-coil peptide GCN4-p1, was probed by mutational analysis. A series of quadruple amino acid replacements that spanned the helix propensity scale were made at the four external f positions in the heptad repeat. Equilibrium and kinetic circular dichroism studies demonstrate that both the stability and the unfolding and refolding rate constants vary with helix propensity but also reflect interactions of the altered side-chains with their local environments. Pairwise replacements and fragment studies show that the two C-terminal heptads are the likely source of the nucleating helices. Helix-helix recognition between preformed elements of secondary structure plays an important role in this fundamental folding reaction.     

Crystal structure of a super leucine zipper,an extended two‐stranded super long coiled coil

Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 Å resolution. The peptide monomer shows a helix trunk with short curved N‐ and C‐termini. In the crystal, two monomers cross in 35° and form an X‐shaped dimer, and each X‐shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two‐stranded, parallel, super long coiled coil rather than a discrete, two‐helix coiled coil of the wild‐type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild‐type leucine zipper, the N‐terminus of the mutant has a dramatic conformational change and the C‐terminus has one more residue Glu 32 determined. The mutant X‐shaped dimer has a large crossing angle of 35° instead of 18° in the wild‐type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self‐assembling protein fibers.     

Automated design of the surface positions of protein helices.

Using a protein design algorithm that quantitatively considers side-chain interactions, the design of surface residues of alpha helices was examined. Three scoring functions were tested: a hydrogen-bond potential, a hydrogen-bond potential in conjunction with a penalty for uncompensated burial of polar hydrogens, and a hydrogen-bond potential in combination with helix propensity. The solvent exposed residues of a homodimeric coiled coil based on GCN4-p1 were designed by using the Dead-End Elimination Theorem to find the optimal amino acid sequence for each scoring function. The corresponding peptides were synthesized and characterized by circular dichroism spectroscopy and size exclusion chromatography. The designed peptides were dimeric and nearly 100% helical at 1 degree C, with melting temperatures from 69-72 degrees C, over 12 degrees C higher than GCN4-p1, whereas a random hydrophilic sequence at the surface positions produced a peptide that melted at 15 degrees C. Analysis of the designed sequences suggests that helix propensity is the key factor in sequence design for surface helical positions.     

Conformational specificity of the lac repressor coiled-coil tetramerization domain

Predictive understanding of how the folded, functional shape of a native protein is encoded in the linear sequence of its amino acid residues remains an unsolved challenge in modern structural biology. Antiparallel four-stranded coiled coils are relatively simple protein structures that embody a heptad sequence repeat and rich diversity for tertiary packing of alpha-helices. To explore specific sequence determinants of the lac repressor coiled-coil tetramerization domain, we have engineered a set of buried nonpolar side chains at the a-, d-, and e-positions into the hydrophobic interior of the dimeric GCN4 leucine zipper. Circular dichroism and equilibrium ultracentrifugation studies show that this core variant (GCN4-pAeLV) forms a stable tetrameric structure with a reversible and highly cooperative thermal unfolding transition. The X-ray crystal structure at 1.9 A reveals that GCN4-pAeLV is an antiparallel four-stranded coiled coil of the lac repressor type in which the a, d, and e side chains associate by means of combined knobs-against-knobs and knobs-into-holes packing with a characteristic interhelical offset of 0.25 heptad. Comparison of the side chain shape and packing in the antiparallel tetramers shows that the burial of alanine residues at the e positions between the neighboring helices of GCN4-pAeLV dictates both the antiparallel orientation and helix offset. This study fills in a gap in our knowledge of the determinants of structural specificity in antiparallel coiled coils and improves our understanding of how specific side chain packing forms the teritiary structure of a functional protein.     

Folding of dimeric methionine adenosyltransferase III: identification of two folding intermediates

Methionine adenosyl transferase (MAT) is an essential enzyme that synthesizes AdoMet. The liver-specific MAT isoform, MAT III, is a homodimer of a 43.7-kDa subunit that organizes in three nonsequential alpha-beta domains. Although MAT III structure has been recently resolved, little is known about its folding mechanism. Equilibrium unfolding and refolding of MAT III, and the monomeric mutant R265H, have been monitored using different physical parameters. Tryptophanyl fluorescence showed a three-state folding mechanism. The first unfolding step was a folding/association process as indicated by its dependence on protein concentration. The monomeric folding intermediate produced was the predominant species between 1.5 and 3 m urea. It had a relatively compact conformation with tryptophan residues and hydrophobic surfaces occluded from the solvent, although its N-terminal region may be very unstructured. The second unfolding step monitored the denaturation of the intermediate. Refolding of the intermediate showed first order kinetics, indicating the presence of a kinetic intermediate within the folding/association transition. Its presence was confirmed by measuring the 1,8-anilinonaphtalene-8-sulfonic acid binding in the presence of tripolyphosphate. We propose that the folding rate-limiting step is the formation of an intermediate, probably a structured monomer with exposed hydrophobic surfaces, that rapidly associates to form dimeric MAT III.     

Rough energy landscapes in protein folding: dimeric E. coli Trp repressor folds through three parallel channels

The folding mechanism of the dimeric Escherichia coli Trp repressor (TR) is a kinetically complex process that involves three distinguishable stages of development. Following the formation of a partially folded, monomeric ensemble of species, within 5 ms, folding to the native dimer is controlled by three kinetic phases. The rate-limiting step in each phase is either a non-proline isomerization reaction or a dimerization reaction, depending on the final denaturant concentration. Two approaches have been employed to test the previously proposed folding mechanism of TR through three parallel channels: (1) unfolding double-jump experiments demonstrate that all three folding channels lead directly to native dimer; and (2) the differential stabilization of the transition state for the final step in folding and the native dimer, by the addition of salt, shows that all three channels involve isomerization of a dimeric species. A refined model for the folding of Trp repressor is presented, in which all three channels involve a rapid dimerization reaction between partially folded monomers followed by the isomerization of the dimeric intermediates to yield native dimer. The ensemble of partially folded monomers can be captured at equilibrium by low pH; one-dimensional proton NMR spectra at pH 2.5 demonstrate that monomers exist in two distinct, slowly interconverting conformations. These data provide a potential structural explanation for the three-channel folding mechanism of TR: random association of two different monomeric forms, which are distinguished by alternative packing modes of the core dimerization domain and the DNA-binding, helix-turn-helix, domain. One, perhaps both, of these packing modes contains non-native contacts.     

Pressure-jump studies of the folding/unfolding of trp repressor.

The dimeric protein, trp apo-repressor of Escherichia coli has been subjected to high hydrostatic pressure under a variety of conditions, and the effects have been monitored by fluorescence spectroscopic and infra-red absorption techniques. Under conditions of micromolar protein concentration and low, non-denaturing concentrations of guanidinium hydrochloride (GuHCl), tryptophan and 8-anilino-1-naphthalene sulfonate (ANS) fluorescence detected high pressure profiles demonstrate that pressures below 3 kbar result in dissociation of the dimer to a monomeric species that presents no hydrophobic binding sites for ANS. The FTIR-detected high pressure profile obtained under significantly different solution conditions (30 mM trp repressor in absence of denaturant) exhibits a much smaller pressure dependence than the fluorescence detected profiles. The pressure-denatured form obtained under the FTIR conditions retains about 50 % alpha-helical structure. From this we conclude that the secondary structure present in the high pressure state achieved under the conditions of the fluorescence experiments is at least as disrupted as that achieved under FTIR conditions. Fluorescence-detected pressure-jump relaxation studies in the presence of non-denaturing concentrations of GuHCl reveal a positive activation volume for the association/folding reaction and a negative activation volume for dissociation/unfolding reaction, implicating dehydration as the rate-limiting step for association/folding and hydration as the rate-limiting step for unfolding. The GuHCl concentration dependence of the kinetic parameters place the transition state at least half-way along the reaction coordinate between the unfolded and folded states. The temperature dependence of the pressure-jump fluorescence-detected dissociation/unfolding reaction in the presence of non-denaturing GuHCl suggests that the curvature in the temperature dependence of the stability arises from non-Arrhenius behavior of the folding rate constant, consistent with a large decrease in heat capacity upon formation of the transition state from the unfolded state. The decrease in the equilibrium volume change for folding with increasing temperature (due to differences in thermal expansivity of the folded and unfolded states) arises from a decrease in the absolute value for the activation volume for unfolding, thus indicating that the thermal expansivity of the transition state is similar to that of the unfolded state.     

A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper.

The effects of different salts (LiCl, NaCl, ChoCl, KF, KCl, and KBr) on the structural stability of a 33-residue peptide corresponding to the leucine zipper region of GCN4 have been studied by high-sensitivity differential scanning calorimetry. These experiments have allowed an estimation of the salt dependence of the thermodynamic parameters that define the stability of the coiled coil. Independent of the nature of the salt, a destabilization of the coiled coil is always observed upon increasing salt concentration up to a maximum of approximately 0.5 M, depending on the specific cation or anion. At higher salt concentrations, this effect is reversed and a stabilization of the leucine zipper is observed. The effect of salt concentration is primarily entropic, judging from the lack of a significant salt dependence of the transition enthalpy. The salt dependence of the stability of the peptide is complex, suggesting the presence of specific salt effects at high salt concentrations in addition to the nonspecific electrostatic effects that are prevalent at lower salt concentrations. The data is consistent with the existence of specific interactions between anions and peptide with an affinity that follows a reverse size order (F- > Cl- > Br-). Under all conditions studied, the coiled coil undergoes reversible thermal unfolding that can be well represented by a reaction of the form N2<==>2U, indicating that the unfolding is a two-state process in which the helices are only stable when they are in the coiled coil conformation.