Probing the high energy states in proteins by proteolysis

Conserved Asp-137 imparts flexibility to tropomyosin and affects function

Tropomyosin (Tm) is an alpha-helical coiled-coil that controls muscle contraction by sterically regulating the myosin-actin interaction. Tm moves between three states on F-actin as either a uniform or a non-uniform semi-flexible rod. Tm is stabilized by hydrophobic residues in the "a" and "d" positions of the heptad repeat. The highly conserved Asp-137 is unusual in that it introduces a negative charge on each chain in a position typically occupied by hydrophobic residues. The occurrence of two charged residues in the hydrophobic region is expected to destabilize the region and impart flexibility. To determine whether this region is unstable, we have substituted hydrophobic Leu for Asp-137 and studied changes in Tm susceptibility to limited proteolysis by trypsin and changes in regulation. We found that native and Tm controls that contain Asp-137 were readily cleaved at Arg-133 with t 1/2 of 5 min. In contrast, the Leu-137 mutant was not cleaved under the same conditions. Actin stabilized Tm, causing a 10-fold reduction in the rate of cleavage at Arg-133. The actin-myosin subfragment S1 ATPase activity was greater for the Leu mutant compared with controls in the absence of troponin and in the presence of troponin and Ca2+. We conclude that the highly conserved Asp-137 destabilizes the middle of Tm, resulting in a more flexible region that is important for the cooperative activation of the thin filament by myosin. We thus have shown a link between the dynamic properties of Tm and its function.

Conformational equilibria and rates of localized motion within hepatitis B virus capsids

Functional analysis of hepatitis B virus (HBV) core particles has associated a number of biological roles with the C terminus of the capsid protein. One set of functions require the C terminus to be on the exterior of the capsid, while others place this domain on the interior. According to the crystal structure of the capsid, this segment is strictly internal to the capsid shell and buried at a protein-protein interface. Using kinetic hydrolysis, a form of protease digestion assayed by SDS-PAGE and mass spectrometry, the structurally and biologically important C-terminal region of HBV capsid protein assembly domain (Cp149, residues 1-149) has been shown to be dynamic in both dimer and capsid forms. HBV is an enveloped virus with a T=4 icosahedral core that is composed of 120 copies of a homodimer capsid protein. Free dimer and assembled capsid forms of the protein are readily hydrolyzed by trypsin and thermolysin, around residues 127-128, indicating that this region is dynamic and exposed to the capsid surface. The measured conformational equilibria have an opposite temperature dependence between free dimer and assembled capsid. This work helps to explain the previously described allosteric regulation of assembly and functional properties of a buried domain. These observations make a critical connection between structure, dynamics, and function: made possible by the first quantitative measurements of conformational equilibria and rates of conversion between protein conformers for a megaDalton complex.

Comparison of Proteolytic Susceptibility in Phosphoglycerate Kinases from Yeast and E. coli: Modulation of Conformational Ensembles Without Altering Structure or Stability

Escherichia coli phosphoglycerate kinase (PGK) is resistant to proteolytic cleavage while the yeast homolog from Saccharomyces cerevisiae is not. We have explored the biophysical basis of this surprising difference. The sequences of these homologs are 39% identical and 56% similar. Determination of the crystal structure for the E. coli protein and comparison to the previously solved yeast structure reveals that the two proteins have extremely similar tertiary structures, and their global stabilities determined by equilibrium denaturation are also very similar. The extrapolated unfolding rate of E. coli PGK is, however, 10(5) slower than that of the yeast homolog. This surprisingly large difference in unfolding rates appears to arise from a divergence in the extent of cooperativity between the two structural domains (the N and C-domains) that make up these kinases. This is supported by: (1) the C-domain of E. coli PGK cannot be expressed or fold independently of the N-domain, while both domains of the yeast protein fold in isolation into stable structures and (2) the energetics and kinetics of the proteolytically sensitive state of E. coli PGK match those for global unfolding. This suggests that proteolysis occurs from the globally unfolded state of E. coli PGK, while the characteristics defining the yeast homolog suggest that proteolysis occurs upon unfolding of only the C-domain, with the N-domain remaining folded and consequently resistant to cleavage.

Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis

Native states of proteins are flexible, populating more than just the unique native conformation. The energetics and dynamics resulting from this conformational ensemble are inherently linked to protein function and regulation. Proteolytic susceptibility is one feature determined by this conformational energy landscape. As an attempt to investigate energetics of proteins on a proteomic scale, we challenged the Escherichia coli proteome with extensive proteolysis and determined which proteins, if any, have optimized their energy landscape for resistance to proteolysis. To our surprise, multiple soluble proteins survived the challenge. Maltose binding protein, a survivor from thermolysin digestion, was characterized by in vitro biophysical studies to identify the physical origin of proteolytic resistance. This experimental characterization shows that kinetic stability is responsible for the unusual resistance in maltose binding protein. The biochemical functions of the identified survivors suggest that many of these proteins may have evolved extreme proteolytic resistance because of their critical roles under stressed conditions. Our results suggest that under functional selection proteins can evolve extreme proteolysis resistance by modulating their conformational energy landscapes without the need to invent new folds, and that proteins can be profiled on a proteomic scale according to their energetic properties by using proteolysis as a structural probe.

Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior

Kinetically stable proteins are unique in that their stability is determined solely by kinetic barriers rather than by thermodynamic equilibria. To better understand how kinetic stability promotes protein survival under extreme environmental conditions, we analyzed the unfolding behavior and determined the structure of Nocardiopsis alba Protease A (NAPase), an acid-resistant, kinetically stable protease, and compared these results with a neutrophilic homolog, alpha-lytic protease (alphaLP). Although NAPase and alphaLP have the same number of acid-titratable residues, kinetic studies revealed that the height of the unfolding free energy barrier for NAPase is less sensitive to acid than that of alphaLP, thereby accounting for NAPase's improved tolerance of low pH. A comparison of the alphaLP and NAPase structures identified multiple salt-bridges in the domain interface of alphaLP that were relocated to outer regions of NAPase, suggesting a novel mechanism of acid stability in which acid-sensitive electrostatic interactions are rearranged to similarly affect the energetics of both the native state and the unfolding transition state. An acid-stable variant of alphaLP in which a single interdomain salt-bridge is replaced with a corresponding intradomain NAPase salt-bridge shows a dramatic >15-fold increase in acid resistance, providing further evidence for this hypothesis. These observations also led to a general model of the unfolding transition state structure for alphaLP protease family members in which the two domains separate from each other while remaining relatively intact themselves. These results illustrate the remarkable utility of kinetic stability as an evolutionary tool for developing longevity over a broad range of harsh conditions.

Acid-induced unfolding kinetics in simulated gastric digestion of proteins

Stability in simulated gastric fluid (SGF) is used as one element in a weight-of-evidence evaluation aimed at determining if a novel protein present in food represents an allergenic risk. The SGF assay is designed to measure the susceptibility of a protein to the enzyme pepsin under acidic conditions, and results are often considered to be primarily a reflection of the vulnerability of a protein to pepsin hydrolysis. However, proteins may not be susceptible to protease cleavage in their native folded conformation, and several studies confirm that protein unfolding is often a prerequisite for pepsinolysis. Here, we explore protein unfolding kinetics as a limiting factor in the digestion of proteins in SGF. Theoretical digestion patterns generated using consecutive and simultaneous exponential models, and the fit of a two stage consecutive exponential model (unfolding followed by pepsinolysis) to laboratory data, support unfolding kinetics as playing a critical role in determining the speed at which many proteins digest in SGF. Results also support modeling of the terminal phase of digestion with a single exponential decline as being a good stability estimate for the most recalcitrant protein form.

Digestion assays in allergenicity assessment of transgenic proteins

The food-allergy risk assessment for transgenic proteins expressed in crops is currently based on a weight-of-evidence approach that holistically considers multiple lines of evidence. This approach recognizes that no single test or property is known to distinguish allergens from nonallergens. The stability of a protein to digestion, as predicted by an in vitro simulated gastric fluid assay, currently is used as one element in the risk assessment process. A review of the literature on the use of the simulated gastric fluid assay to predict the allergenic status of proteins suggests that more extensive kinetic studies with well-characterized reference proteins are required before the predictive value of this assay can be adequately judged.

Native state energetics of the Src SH2 domain: evidence for a partially structured state in the denatured ensemble

We have defined the free-energy profile of the Src SH2 domain using a variety of biophysical techniques. Equilibrium and kinetic experiments monitored by tryptophan fluorescence show that Src SH2 is quite stable and folds rapidly by a two-state mechanism, without populating any intermediates. Native state hydrogen-deuterium exchange confirms this two-state behavior; we detect no cooperative partially unfolded forms in equilibrium with the native conformation under any conditions. Interestingly, the apparent stability of the protein from hydrogen exchange is 2 kcal/mol greater than the stability determined by both equilibrium and kinetic studies followed by fluorescence. Native-state proteolysis demonstrates that this "super protection" does not result from a deviation from the linear extrapolation model used to fit the fluorescence data. Instead, it likely arises from a notable compaction in the unfolded state under native conditions, resulting in an ensemble of conformations with substantial solvent exposure of side chains and flexible regions sensitive to proteolysis, but backbone amides that exchange with solvent approximately 30-fold slower than would be expected for a random coil. The apparently simple behavior of Src SH2 in traditional unfolding studies masks the significant complexity present in the denatured-state ensemble.

Highly stable mutants of human fibroblast growth factor-1 exhibit prolonged biological action

Fibroblast growth factor 1 (FGF-1) shows strong angiogenic, osteogenic and tissue-injury repair properties that might be relevant to medical applications. Since FGF-1 is partially unfolded at physiological temperature we decided to increase significantly its conformational stability and test how such an improvement will affect its biological function. Using an homology approach and rational strategy we designed two new single FGF-1 mutations: Q40P and S47I that appeared to be the most strongly stabilizing substitutions among those reported so far, increasing the denaturation temperature by 7.8 deg. C and 9.0 deg. C, respectively. As our goal was to produce highly stable variants of the growth factor, we combined these two mutations with five previously described stabilizing substitutions. The multiple mutants showed denaturation temperatures up to 27 deg. C higher than the wild-type and exhibited full additivity of the mutational effects. All those mutants were biologically competent in several cell culture assays, maintaining typical FGF-1 activities, such as binding to specific cell surface receptors and activation of downstream signaling pathways. Thus, we demonstrate that the low denaturation temperature of wild-type FGF-1 is not related to its fundamental cellular functions, and that FGF-1 action is not affected by its stability. A more detailed analysis of the biological behavior of stable FGF-1 mutants revealed that, compared with the wild-type, their mitogenic properties, as probed by the DNA synthesis assay, were significantly increased in the absence of heparin, and that their half-lives were extensively prolonged. We found that the biological action of the mutants was dictated by their susceptibility to proteases, which strongly correlated with the stability. Mutants which were much more resistant to proteolytic degradation always displayed a significant improvement in the half-life and mitogenesis. Our results show that engineered stable growth factor variants exhibit enhanced and prolonged activity, which can be advantageous in terms of the potential therapeutic applications of FGF-1.

Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding

Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's stability typically requires biophysical instrumentation and substantial quantities of purified protein, which has limited the use of this technique as a general laboratory method. We report here a simple new method for determining protein stability by using pulse proteolysis with varying concentrations of denaturant. Pulse proteolysis is designed to digest only the unfolded proteins in an equilibrium mixture of folded and unfolded proteins that relaxes on a time scale longer than the proteolytic pulse. We used this method to study the stabilities of Escherichia coli ribonuclease H and its variants, both in purified form and directly from cell lysates. The DeltaG(unf) degrees values obtained by this technique were in agreement with those determined by traditional methods. We also successfully used this method to monitor the binding of maltose-binding protein to maltose, as well as to rapidly screen cognate ligands for this protein. The simplicity of pulse proteolysis suggests that it is an excellent strategy for the high-throughput determination of protein stability in protein engineering and drug discovery applications.