Backbone dynamics of the monomeric lambda repressor denatured state ensemble under nondenaturing conditions

NMR insights into folding and self-association of Plasmodium falciparum P2

The eukaryotic 60S-ribosomal stalk is composed of acidic ribosomal proteins (P1 and P2) and neutral protein P0, which are thought to be associated as a pentameric structure, [2P1, 2P2, P0]. Plasmodium falciparum P2 (PfP2) appears to play additional non-ribosomal functions associated with its tendency for homo-oligomerization. Recombinant bacterially expressed PfP2 protein also undergoes self-association, as shown by SDS-PAGE analysis and light scattering studies. Secondary structure prediction algorithms predict the native PfP2 protein to be largely helical and this is corroborated by circular dichroism investigation. The ¹H-¹⁵N HSQC spectrum of native P2 showed only 43 cross peaks compared to the expected 138. The observed peaks were found to belong to the C-terminal region, suggesting that this segment is flexible and solvent exposed. In 9 M urea denaturing conditions the chain exhibited mostly non-native β structural propensity. ¹⁵N Relaxation data for the denatured state indicated substantial variation in ms-µs time scale motion along the chain. Average area buried upon folding (AABUF) calculations on the monomer enabled identification of hydrophobic patches along the sequence. Interestingly, the segments of slower motion in the denatured state coincided with these hydrophobic patches, suggesting that in the denatured state the monomeric chain undergoes transient hydrophobic collapse. The implications of these results for the folding mechanism and self-association of PfP2 are discussed.

Conformational properties of the unfolded state of Im7 in nondenaturing conditions

The unfolded ensemble in aqueous solution represents the starting point of protein folding. Characterisation of this species is often difficult since the native state is usually predominantly populated at equilibrium. Previous work has shown that the four-helix protein, Im7 (immunity protein 7), folds via an on-pathway intermediate. While the transition states and folding intermediate have been characterised in atomistic detail, knowledge of the unfolded ensemble under the same ambient conditions remained sparse. Here, we introduce destabilising amino acid substitutions into the sequence of Im7, such that the unfolded state becomes predominantly populated at equilibrium in the absence of denaturant. Using far- and near-UV CD, fluorescence, urea titration and heteronuclear NMR experiments, we show that three amino acid substitutions (L18A-L19A-L37A) are sufficient to prevent Im7 folding, such that the unfolded state is predominantly populated at equilibrium. Using measurement of chemical shifts, (15)N transverse relaxation rates and sedimentation coefficients, we show that the unfolded species of L18A-L19A-L37A deviates significantly from random-coil behaviour. Specifically, we demonstrate that this unfolded species is compact (R(h)=25 Å) relative to the urea-denatured state (R(h)≥30 Å) and contains local clusters of hydrophobic residues in regions that correspond to the four helices in the native state. Despite these interactions, there is no evidence for long-range stabilising tertiary interactions or persistent helical structure. The results reveal an unfolded ensemble that is conformationally restricted in regions of the polypeptide chain that ultimately form helices I, II and IV in the native state.

Folding of a tryptophan zipper peptide investigated on the basis of the nuclear Overhauser effect and thermal denaturation

Short, secondary-structure-containing peptides are suitable models for the study of protein folding due to their relative simplicity. Here, we investigate thermal denaturation of the tryptophan zipper peptide, trpzip4, a peptide that forms a β-hairpin in solution. In order to monitor the thermal denaturation of peptides or small proteins, chemical shift values of H(α) or H(N) may be used. However, various factors other than secondary structure can influence chemical shift values, such as side-chain orientation of nearby aromatic residues. Nuclear Overhauser effect (NOE) intensity from backbone interproton cross peaks is an alternative way to study thermal denaturation, as long as various factors that give rise to a change in NOE intensity upon changing the temperature are considered. As a relative indicator for denaturation, we define a cutoff temperature, where half of the initial NOE intensity is lost for each backbone interproton cross peak. For trpzip4, this cutoff temperature is highest for residues in the central part of the structure and lowest for residues near the termini. These observations support the notion that the structure of the trpzip4 peptide is stabilized by a hydrophobic cluster formed by tryptophan residues located in the central region of the β-hairpin.

The fast and the slow: folding and trapping of λ6-85

Molecular dynamics simulations combining many microsecond trajectories have recently predicted that a very fast folding protein like lambda repressor fragment λ(6-85) D14A could have a slow millisecond kinetic phase. We investigated this possibility by detecting temperature-jump relaxation to 5 ms. While λ(6-85) D14A has no significant slow phase, two even more stable mutants do. A slow phase of λ(6-85) D14A does appear in mild denaturant. The experimental data and computational modeling together suggest the following hypothesis: λ(6-85) takes only microseconds to reach its native state from an extensively unfolded state, while the latter takes milliseconds to reach compact β-rich traps. λ(6-85) is not only thermodynamically but also kinetically protected from reaching such "intramolecular amyloids" while folding.

Uncovering specific electrostatic interactions in the denatured states of proteins

The stability and folding of proteins are modulated by energetically significant interactions in the denatured state that is in equilibrium with the native state. These interactions remain largely invisible to current experimental techniques, however, due to the sparse population and conformational heterogeneity of the denatured-state ensemble under folding conditions. Molecular dynamics simulations using physics-based force fields can in principle offer atomistic details of the denatured state. However, practical applications are plagued with the lack of rigorous means to validate microscopic information and deficiencies in force fields and solvent models. This study presents a method based on coupled titration and molecular dynamics sampling of the denatured state starting from the extended sequence under native conditions. The resulting denatured-state pK(a)s allow for the prediction of experimental observables such as pH- and mutation-induced stability changes. I show the capability and use of the method by investigating the electrostatic interactions in the denatured states of wild-type and K12M mutant of NTL9 protein. This study shows that the major errors in electrostatics can be identified by validating the titration properties of the fragment peptides derived from the sequence of the intact protein. Consistent with experimental evidence, our simulations show a significantly depressed pK(a) for Asp(8) in the denatured state of wild-type, which is due to a nonnative interaction between Asp(8) and Lys(12). Interestingly, the simulation also shows a nonnative interaction between Asp(8) and Glu(48) in the denatured state of the mutant. I believe the presented method is general and can be applied to extract and validate microscopic electrostatics of the entire folding energy landscape.

NMR characterization of hydrophobic collapses in amyloidogenic unfolded states and their implications for amyloid formation

NMR spectroscopy was used to characterize hydrophobic clusters in amyloidogenic unfolded states of a protein and their implications for amyloid formation. Three local hydrophobic clusters were observed in the amyloidogenic state of the phosphatidylinositol 3-kinase (PI3K) SH3 domain. Our NMR studies showed that residues with high average area buried upon folding (AABUF) parameter collapsed to form the clusters. Interestingly, the hydrophobic collapses were not stabilized by long-range tertiary interactions among the clusters that were typically observed in non-amyloidogenic unfolded states of various proteins. The lack of the long-range interactions may be a critical property of the amyloidogenic unfolded state. The SH3 domain was also engineered to disrupt one of the clusters by a single-point mutagenesis (W55G), which allowed us to investigate the effect of the clustering on folding and misfolding. The mutant form of the SH3 domain was not able to fold under folding conditions of the wild type protein (pH 3.6-4.0), supporting the cooperative folding hypothesis. However, aggregation properties of the mutant form were not influenced by the mutation, suggesting the SH3 domain forms amyloid via a non-cooperative process.

Analysis of the free-energy surface of proteins from reversible folding simulations

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

The process of protein folding is a complex transition from a disordered to an ordered state. Here, we simulate a specific fast-folding protein at the point at which the native and denatured states are at equilibrium and show that obtaining an accurate description of the mechanisms of folding and unfolding is far from trivial. Using simple quantities which quantify the degree of native order is, in the case of this protein, clearly misleading. We show that an unbiased representation of the free-energy surface can be obtained; using such a representation we are able to redesign the landscape and thus modify, upon site-specific “mutations”, the folding and unfolding rates. This leads us to formulate a hypothesis to explain the very fast folding of many proteins.

Structural mobility of the monomeric C-terminal domain of the HIV-1 capsid protein

The capsid protein of HIV-1 (p24) (CA) forms the mature capsid of the human immunodeficiency virus. Capsid assembly involves hexamerization of the N-terminal domain and dimerization of the C-terminal domain of CA (CAC), and both domains constitute potential targets for anti-HIV therapy. CAC homodimerization occurs mainly through its second helix, and it is abolished when its sole tryptophan is mutated to alanine. This mutant, CACW40A, resembles a transient monomeric intermediate formed during dimerization. Its tertiary structure is similar to that of the subunits in the dimeric, non-mutated CAC, but the segment corresponding to the second helix samples different conformations. The present study comprises a comprehensive examination of the CACW40A internal dynamics. The results obtained, with movements sampling a wide time regime (from pico- to milliseconds), demonstrate the high flexibility of the whole monomeric protein. The conformational exchange phenomena on the micro-to-millisecond time scale suggest a role for internal motions in the monomer-monomer interactions and, thus, flexibility of the polypeptide chain is likely to contribute to the ability of the protein to adopt different conformational states, depending on the biological environment.