Protein kinetic stability

Impact of translational error-induced and error-free misfolding on the rate of protein evolution

Theoretical calculations suggest that, in addition to translational error-induced protein misfolding, a non-negligible fraction of misfolded proteins are error free.

We propose that the anticorrelation between the expression level of a protein and its rate of sequence evolution be explained by an overarching protein-misfolding-avoidance hypothesis that includes selection against both error-induced and error-free protein misfolding, and verify this model by a molecular-level evolutionary simulation.

We provide strong empirical evidence for the protein-misfolding-avoidance hypothesis, including a positive correlation between protein expression level and stability, enrichment of misfolding-minimizing codons and amino acids in highly expressed genes, and stronger evolutionary conservation of residues in which nonsynonymous changes are more likely to increase protein misfolding.

The rate of protein sequence evolution has long been of central interest to molecular evolutionists. Different proteins of the same species evolve at vastly different rates, which is commonly explained by a variation in functional constraint among different proteins (Kimura and Ohta, 1974). However, it is unclear how to quantify the functional constraint of a protein from the knowledge of its function. In the past decade, various types of genomic data from model organisms have been examined to look for the determinants of the rate of protein sequence evolution. The most unexpected discovery was a very strong anticorrelation between the expression level and evolutionary rate of a protein (E–R anticorrelation) (Pal et al, 2001). The prevailing explanation of the E–R anticorrelation is the translational robustness hypothesis (Drummond et al, 2005). This hypothesis posits that mistranslation induces protein misfolding, which is toxic to cells (Figure 1). Consequently, highly expressed proteins are under stronger pressures to be translationally robust and thus are more constrained in sequence evolution. However, the impact of the other source of misfolded proteins, translational error-free proteins (Figure 1), has not been evaluated. By theoretical calculation, computer simulation, and empirical data analysis, we examined the role of selection against both error-induced and error-free protein misfolding in creating the E–R correlation.

Our theoretical calculations suggested that a non-negligible fraction of misfolded proteins are error free. We estimated that when a protein is not very stable, on average ∼20% of misfolded molecules are error free. However, when a protein is very stable, this fraction reduces to ∼5%, which is probably a result of natural selection against protein misfolding.

We conducted a molecular-level evolutionary simulation (Figure 2A) using three different schemes: error-induced misfolding only, error-free misfolding only, and both types of misfolding. As expected, results from the first simulation are similar to those from a previous study that considers only error-induced misfolding (Drummond and Wilke, 2008). Interestingly, the second and third simulations can also generate the same patterns, including a positive correlation between the protein expression level and the unfolding energy (ΔG) of the error-free protein (Figure 2B), a negative correlation between the expression level and the fraction of protein molecules that misfold after being mistranslated (Figure 2C), a negative correlation between ΔG and the evolutionary rate (Figure 2D), and a negative correlation between the expression level and the evolutionary rate (i.e., the E–R anticorrelation) (Figure 2E). Furthermore, we found that selection against protein misfolding is more effective in reducing error-free misfolding than error-induced misfolding.

Based on these results, we propose that an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the prevailing translational robustness hypothesis, which considers only error-induced misfolding. We tested three key predictions of the protein-misfolding-avoidance hypotheses using yeast data. First, we showed that, consistent with our prediction, a positive correlation exists between the protein expression level and stability, which is measured by the unfolding energy or melting temperature. In addition, protein expression level is negatively correlated with protein aggregation propensity. Second, we found that codons minimizing protein misfolding are used more frequently in highly expressed proteins than in lowly expressed ones. Third, we showed that, within the same protein, amino acid residues in which random nonsynonymous mutations are more likely to increase protein misfolding are evolutionarily more conserved.

Together, these results provide unambiguous evidence that avoidance of both error-induced and error-free protein misfolding is a major source of the E–R anticorrelation and that protein stability and mistranslation have important roles in protein evolution.

What determines the rate of protein evolution is a fundamental question in biology. Recent genomic studies revealed a surprisingly strong anticorrelation between the expression level of a protein and its rate of sequence evolution. This observation is currently explained by the translational robustness hypothesis in which the toxicity of translational error-induced protein misfolding selects for higher translational robustness of more abundant proteins, which constrains sequence evolution. However, the impact of error-free protein misfolding has not been evaluated. We estimate that a non-negligible fraction of misfolded proteins are error free and demonstrate by a molecular-level evolutionary simulation that selection against protein misfolding results in a greater reduction of error-free misfolding than error-induced misfolding. Thus, an overarching protein-misfolding-avoidance hypothesis that includes both sources of misfolding is superior to the translational robustness hypothesis. We show that misfolding-minimizing amino acids are preferentially used in highly abundant yeast proteins and that these residues are evolutionarily more conserved than other residues of the same proteins. These findings provide unambiguous support to the role of protein-misfolding-avoidance in determining the rate of protein sequence evolution.

Chaperoning osteogenesis: new protein-folding disease paradigms

Recent discoveries of severe bone disorders in patients with deficiencies in several endoplasmic reticulum chaperones are reshaping the discussion of type I collagen folding and related diseases. Type I collagen is the most abundant protein in all vertebrates and a crucial structural molecule for bone and other connective tissues. Its misfolding causes bone fragility, skeletal deformity and other tissue failures. Studies of newly discovered bone disorders indicate that collagen folding, chaperones involved in the folding process, cellular responses to misfolding and related bone pathologies might not follow conventional protein folding paradigms. In this review, we examine the features that distinguish collagen folding from that of other proteins and describe the findings that are beginning to reveal how cells manage collagen folding and misfolding. We discuss implications of these studies for general protein folding paradigms, unfolded protein response in cells and protein folding diseases.

Role of low native state kinetic stability and interaction of partially unfolded states with molecular chaperones in the mitochondrial protein mistargeting associated with primary hyperoxaluria

The G170R variant of the alanine:glyoxylate aminotransferase (AGT) is the most common pathogenic allele associated to primary hyperoxaluria type I (PH1), leading to mitochondrial mistargeting when combined with the P11L and I340M polymorphisms (minor allele; AGT(LM)). In this work, we have performed a comparative analysis on the conformation, unfolding energetics and interaction with molecular chaperones between AGT(wt), AGT(LM) and AGT(LRM) (G170R in the minor allele) proteins. Our results show that these three variants share similar conformational and functional properties as folded dimers. However, kinetic stability analyses showed a ≈1,000-fold increased unfolding rate for apo-AGT(LRM) compared to apo-AGT(wt), as well as a reduced folding efficiency upon expression in Escherichia coli. Pyridoxal 5'-phosphate (PLP)-binding provided a 4-5 orders of magnitude enhancement of the kinetic stability for all variants, suggesting a role for kinetic stabilization in pyridoxine-responsive PH1. Conformational studies at mild acidic pH and moderate guanidium concentrations showed the formation of a molten-globule-like unfolding intermediate in all three variants, which do not reactivate to the native state and strongly interact with Hsc70 and Hsp90 chaperones. Additional expression analyses in a mammalian cell-free system at neutral pH showed enhanced interaction of AGT(LRM) with Hsc70 and Hsp90 proteins compared to AGT(wt), suggesting kinetic trapping of the mutant by chaperones along the folding process. Overall, our results suggest that mitochondrial mistargeting of AGT(LRM) may involve the presentation of AGT partially folded states to the mitochondrial import machinery by molecular chaperones, which would be facilitated by the low native state kinetic stability (partially corrected by PLP binding) and kinetic trapping during folding of the AGT(LRM) variant with molecular chaperones.

Co-localization of mutant p53 and amyloid-like protein aggregates in breast tumors

P53 is one of the most important tumor suppressor proteins in human cancers. Mutations in the TP53 gene are common features of malignant tumors and normally correlate to a more aggressive disease. In breast cancer, these gene alterations are present in approximately 20% of cases and are characteristically of missense type. In the present work we describe TP53 mutations in breast cancer biopsies and investigate whether wild and mutant p53 participate in protein aggregates formation in these breast cancer cases. We analyzed 88 biopsies from patients residing in the metropolitan area of Rio de Janeiro, and performed TP53 mutation screening using direct sequencing of exons 5-10. Seventeen mutations were detected, 12 of them were of missense type, 2 nonsenses, 2 deletions and 1 insertion. The presence of TP53 mutation was highly statistically associated to tumor aggressiveness of IDC cases, indicated here by Elston Grade III (p<0.0001). Paraffin embedded breast cancer tissues were analyzed for the presence of p53 aggregates through immunofluorescence co-localization assay, using anti-aggregate primary antibody A11, and anti-p53. Our results show that mutant p53 co-localizes with amyloid-like protein aggregates, depending on mutation type, suggesting that mutant p53 may form aggregates in breast cancer cells, in vivo.

The critical role of the constant region in thermal stability and aggregation of amyloidogenic immunoglobulin light chain

Light chain (LC) amyloidosis (AL) is a fatal disease in which immunoglobulin LC deposit as fibrils. Although the LC amyloid-forming propensity is attributed primarily to the variable region, fibrils also contain full-length LC comprised of variable-joining (V(L)) and constant (C(L)) regions. To assess the role of C(L) in fibrillogenesis, we compared the thermal stability of full-length LC and corresponding V(L) and C(L) fragments. Protein unfolding and aggregation were monitored by circular dichroism and light scattering. A full-length λ6 LC purified from urine of a patient with AL amyloidosis showed irreversible unfolding coupled to aggregation. The transition temperature decreased at slower heating rates, indicating kinetic effects. Next, we studied five recombinant λ6 proteins: full-length amyloidogenic LC, its V(L), germline LC, germline V(L), and C(L). Amyloidogenic and germline proteins showed similar rank order of stability, V(L) < LC < C(L); hence, in the full-length LC, V(L) destabilizes C(L). Amyloidogenic proteins were less stable than their germline counterparts, suggesting that reduction in V(L) stability destabilizes the full-length LC. Thermal unfolding of the full-length amyloidogenic and germline LC required high activation energy and involved irreversible aggregation, yet the unfolding of the isolated V(L) and C(L) fragments was partially reversible. Therefore, compared to their fragments, full-length LCs are more likely to initiate aggregation during unfolding and provide a template for the V(L) deposition. The kinetic barrier for this aggregation is regulated by the stability of the V(L) region. This represents a paradigm shift in AL fibrillogenesis and suggests C(L) region as a potential therapeutic target.

Protein folding pathways and state transitions described by classical equations of motion of an elastic network model

Protein topology defined by the matrix of residue contacts has proved to be a fruitful basis for the study of protein dynamics. The widely implemented coarse-grained elastic network model of backbone fluctuations has been used to describe crystallographic temperature factors, allosteric couplings, and some aspects of the folding pathway. In the present study, we develop a model of protein dynamics based on the classical equations of motion of a damped network model (DNM) that describes the folding path from a completely unfolded state to the native conformation through a single-well potential derived purely from the native conformation. The kinetic energy gained through the collapse of the protein chain is dissipated through a friction term in the equations of motion that models the water bath. This approach is completely general and sufficiently fast that it can be applied to large proteins. Folding pathways for various proteins of different classes are described and shown to correlate with experimental observations and molecular dynamics and Monte Carlo simulations. Allosteric transitions between alternative protein structures are also modeled within the DNM through an asymmetric double-well potential.