Engineering Stabilising β-Sheet Interactions into a Conformationally Flexible Region of the Folding Transition State of Ubiquitin

Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments

Protein loops are frequently considered as critical determinants in protein structure and function. Recent advances in high-throughput methods for DNA sequencing and thermal stability measurement have enabled effective exploration of sequence-structure-function relationships in local protein regions. Using these data-intensive technologies, we investigated the sequence-structure-function relationships of six complementarity-determining regions (CDRs) and ten non-CDR loops in the variable domains of a model vascular endothelial growth factor (VEGF)-binding single-chain antibody variable fragment (scFv) whose sequence had been optimized via a consensus-sequence approach. The results show that only a handful of residues involving long-range tertiary interactions distant from the antigen-binding site are strongly coupled with antigen binding. This implies that the loops are passive regions in protein folding; the essential sequences of these regions are dictated by conserved tertiary interactions and the consensus local loop-sequence features contribute little to protein stability and function.

Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps

The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.

Helix mutations stabilize a late productive intermediate on the folding pathway of ubiquitin

We have investigated the relative placement of rate-limiting energy barriers and the role of productive or obstructive intermediates on the folding pathway of yeast wild-type ubiquitin ( wt-Ub) containing the F45W mutation. To manipulate the folding barriers, we have designed a family of mutants in which stabilizing substitutions have been introduced incrementally on the solvent-exposed surface of the main alpha-helix (residues 23-34), which has a low intrinsic helical propensity in the native sequence. Although the U --> I and I --> N transitions are not clearly delineated in the kinetics of wt-Ub, we show that an intermediate becomes highly populated and more clearly resolved as the predicted stability of the helix increases. The observed acceleration in the rate of folding correlates with helix stability and is consistent with the I-state representing a productive rather than misfolded state. A Leffler analysis of the effects on kinetics of changes in stability within the family of helix mutants results in a biphasic correlation in both the refolding and unfolding rates that suggest a shift from a nucleation-condensation mechanism (weakly stabilized helix) toward a diffusion-collision model (highly stabilized helix). Through the introduction of helix-stabilizing mutations, we are able to engineer a well-resolved I-state on the folding pathway of ubiquitin which is likely to be structurally distinct from that which is only weakly populated on the folding pathway of wild-type ubiquitin.

Roles of beta-turns in protein folding: from peptide models to protein engineering

Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.

Loop anchor modification causes the population of an alternative native state in an SH3-like domain

Many stably folded proteins are proposed to contain long, unstructured loops. A series of hybrid proteins (EbE1-4) containing the folded scaffold of photosystem I accessory protein E (PsaE), an SH3-like protein, and the 40-residue heme-binding loop of cytochrome b(5) was created to inspect the dependence of thermodynamic and kinetic parameters on the residues at the interface of folded and flexible regions. Compared to the simplest hybrid (EbE1), the chimeras differed by Gly insertions (EbE2, EbE3) or an asymmetric four-residue restructuring of loop termini (EbE4). NMR spectroscopy indicated that the chimeras retained the PsaE topology; native and unfolded state solubilities, however, were affected to varying degrees. Thermal and chemical denaturation experiments revealed that the EbE2 and EbE1 constructs resulted in a modest destabilization of the PsaE core, whereas apparent stability was increased by >5 kJ/mol in EbE4. EbE3 aggregated at microM concentrations and was not studied in detail. EbE4 populated two native states (N1 and N2), which differed by hydrophobic core packing and C-terminal interactions. At room temperature, the population ratio ( approximately 3-4:1) favored the state whose spectroscopic properties most resembled those of PsaE (N1). EbE4 also demonstrated altered folding kinetics, displaying multiple slow phases related to the population of intermediates and possibly N2. It was concluded that loop anchors can affect protein properties, including stability, via short-range effects on local structure and long-range communication with the packed hydrophobic core. Modification of the attachment points appears to be a possible stepping stone in the transition from one three-dimensional structure to another.

Fluctuations of primary ubiquitin folding intermediates in a force clamp

Folding experiments of single ubiquitin molecules under force clamp using an atomic force microscope revealed a dynamic long-lived intermediate with nanometer scale end-to-end distance fluctuations along an unexpectedly complex folding pathway. To examine the nature of this intermediate at the atomic level as well as the driving forces that give rise to the observed fluctuations, we performed molecular dynamics refolding simulations of unfolded ubiquitin under constant force. After an initial fast collapse, we find a highly dynamic, broad ensemble of conformations with partial and continuously changing secondary structure and side chain interactions. This ensemble resembles a molten-globule-like state, similar in nature to the previously described non-native state of ubiquitin in solution, but stretched by the external force. The scale of the end-to-end distance fluctuations derived from the simulations compares well with experiment. Transient formation of unspecific and metastable hydrophobic clusters along the chain are found to give rise to the observed end-to-end distance fluctuations. These distinct collapses, interpreted as folding attempts, imply an upper limit for the folding attempt frequency of approximately 10 ns. Our results suggest possible relations between force-induced unfolding and temperature or chemically induced denaturation.

Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin

The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C(alpha)-Gō model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench refolding-times scale as tau(F) approximately exp(f(q)Deltax(F)/k(B)T), where f(q) is the quench force and Deltax(F) approximately 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to Deltax(F) approximately 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state Deltax(UF) approximately 0.24 nm, which is in reasonable agreement with the experimental data.

Model systems for β-hairpins and β-sheets

beta-Sheets and alpha-helices are the two principal secondary structures in proteins. However, our understanding of beta-sheet structure lags behind that of alpha-helices, largely because, until recently, there was no model system to study the beta-sheet secondary structure in isolation. With the development of well-folded beta-hairpins, this is changing rapidly. Recent advances include: increased understanding of the relative contributions of turn, strand and sidechain interactions to beta-hairpin and beta-sheet stability, with the role of aromatic residues as a common subtheme; experimental and theoretical kinetic and thermodynamic studies of beta-hairpin and beta-sheet folding; de novo protein design, including all-beta structures, mixed alpha/beta motifs and switchable systems; and the creation of functional beta-hairpins.

Ubiquitin: a small protein folding paradigm

For the past twenty years, the small, 76-residue protein ubiquitin has been used as a model system to study protein structure, stability, folding and dynamics. In this time, ubiquitin has become a paradigm for both the experimental and computational folding communities. The folding energy landscape is now uniquely characterised with a plethora of information available on not only the native and denatured states, but partially structured states, alternatively folded states and locally unfolded states, in addition to the transition state ensemble. This Perspective focuses on the experimental characterisation of ubiquitin using a comprehensive range of biophysical techniques.

Engineering Diverse Changes in β-Turn Propensities in the N-Terminal β-Hairpin of Ubiquitin Reveals Significant Effects on Stability and Kinetics but a Robust Folding Transition State

Using the N-terminal 17-residue beta-hairpin of ubiquitin as a "host" for mutational studies, we have investigated the influence of the beta-turn sequence on protein stability and folding kinetics by replacing the native G-bulged turn (TLTGK) with more flexible analogues (TG3K and TG5K) and a series of four-residue type I' beta-turn sequences, commonly found in beta-hairpins. Although a statistical analysis of type I' turns demonstrates residue preferences at specific sites, the frequency of occurrence appears to only broadly correlate with experimentally determined protein stabilities. The subsequent engineering of context-dependent non-native tertiary contacts involving turn residues is shown to produce large changes in stability. Relatively few point mutations have been described that probe secondary structure formation in ubiquitin in a manner that is independent of tertiary contacts. To this end, we have used the more rigorous rate-equilibrium free energy relationship (Leffler analysis), rather than the two-point phi value analysis, to show for a family of engineered beta-turn mutants that stability (range of approximately 20 kJ/mol) and folding kinetics (190-fold variation in refolding rate) are linearly correlated (alpha(f) = 0.74 +/- 0.08). The data are consistent with a transition state that is robust with regard to a wide range of statistically favored and disfavored beta-turn mutations and implicate a loosely assembled beta-hairpin as a key template in transition state stabilization with the beta-turn playing a central role.