Some thermodynamic implications for the thermostability of proteins

Rheostatic contributions to protein stability can obscure a position's functional role

Rheostat positions, which can be substituted with various amino acids to tune protein function across a range of outcomes, are a developing area for advancing personalized medicine and bioengineering. Current methods cannot accurately predict which proteins contain rheostat positions or their substitution outcomes. To compare the prevalence of rheostat positions in homologs, we previously investigated their occurrence in two pyruvate kinase (PYK) isozymes. Human liver PYK contained numerous rheostat positions that tuned the apparent affinity for the substrate phosphoenolpyruvate (Kapp-PEP) across a wide range. In contrast, no functional rheostat positions were identified in Zymomonas mobilis PYK (ZmPYK). Further, the set of ZmPYK substitutions included an unusually large number that lacked measurable activity. We hypothesized that the inactive substitution variants had reduced protein stability, precluding detection of Kapp-PEP tuning. Using modified buffers, robust enzymatic activity was obtained for 19 previously-inactive ZmPYK substitution variants at three positions. Surprisingly, both previously-inactive and previously-active substitution variants all had Kapp-PEP values close to wild-type. Thus, none of the three positions were functional rheostat positions, and, unlike human liver PYK, ZmPYK's Kapp-PEP remained poorly tunable by single substitutions. To directly assess effects on stability, we performed thermal denaturation experiments for all ZmPYK substitution variants. Many diminished stability, two enhanced stability, and the three positions showed different thermal sensitivity to substitution, with one position acting as a "stability rheostat." The differences between the two PYK homologs raises interesting questions about the underlying mechanism(s) that permit functional tuning by single substitutions in some proteins but not in others.

Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes

Differential scanning fluorimetry (DSF) is a technique that reports protein thermal stability via the selective recognition of unfolded states by fluorogenic dyes. However, DSF applications remain limited by protein incompatibilities with existing DSF dyes. Here we overcome this obstacle with the development of a protein-adaptive DSF platform (paDSF) that combines a dye library 'Aurora' with a streamlined procedure to identify protein-dye pairs on demand. paDSF was successfully applied to 94% (66 of 70) of proteins, tripling the previous compatibility and delivering assays for 66 functionally and biochemically diverse proteins, including 10 from severe acute respiratory syndrome coronavirus 2. We find that paDSF can be used to monitor biological processes that were previously inaccessible, demonstrated for the interdomain allostery of O-GlcNAc transferase. The chemical diversity and varied selectivities of Aurora dyes suggest that paDSF functionality may be readily extended. paDSF is a generalizable tool to interrogate protein stability, dynamics and ligand binding.

Chemoenzymatic indican for light-driven denim dyeing

Blue denim, a billion-dollar industry, is currently dyed with indigo in an unsustainable process requiring harsh reducing and alkaline chemicals. Forming indigo directly in the yarn through indican (indoxyl-β-glucoside) is a promising alternative route with mild conditions. Indican eliminates the requirement for reducing agent while still ending as indigo, the only known molecule yielding the unique hue of blue denim. However, a bulk source of indican is missing. Here, we employ enzyme and process engineering guided by techno-economic analyses to develop an economically viable drop-in indican synthesis technology. Rational engineering of PtUGT1, a glycosyltransferase from the indigo plant, alleviated the severe substrate inactivation observed with the wildtype enzyme at the titers needed for bulk production. We further describe a mild, light-driven dyeing process. Finally, we conduct techno-economic, social sustainability, and comparative life-cycle assessments. These indicate that the presented technologies have the potential to significantly reduce environmental impacts from blue denim dyeing with only a modest cost increase.

Protocol for performing and optimizing differential scanning fluorimetry experiments

Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.

Deconvolution Analysis of the Non-Ionic Iomeprol, Iobitridol and Iodixanol Contrast Media-Treated Human Whole Blood Thermograms: A Comparative Study

To study the effect of non-ionic contrast media on anticoagulated and non-anticoagulated human whole blood samples, calorimetric measurements were performed. The anticoagulated plasma showed the greatest fall in the total ΔH after Iodixanol treatment. The plasma-free erythrocytes revealed a pronounced shift in the Tmax and a decrease in the ΔH of hemoglobin and transferrin. The total ΔH of Iodixanol treatment showed the highest decline, while Iomeprol and Iobitridol had fewer adverse effects. Similarly, the non-anticoagulated samples revealed a decrease both in the Tmax and the ΔH of albumin and immunoglobulin-specific transitions. The total ΔH showed that Iodixanol had more influence on the serum. The serum-free erythrocyte samples resulted in a significant drop in the Tmax of erythrocyte and transferrin (~5-6 °C). The ΔH of deconvolved hemoglobin and transferrin decreased considerably; however, the ΔH of albumin increased. Surprisingly, compared to Iomeprol and Iobitridol treatments, the total ΔH of Iodixanol was less pronounced in the non-anticoagulated erythrocyte samples. In sum, each non-ionic contrast medium affected the thermal stability of anticoagulated and non-anticoagulated erythrocyte proteins. Interestingly, Iodixanol treatment caused more significant effects. These findings suggest that conformational changes in blood components can occur, which can potentially lead to the increased prevalence of cardiovascular dysfunctions and blood clotting.

Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease

Nirmatrelvir is an orally available inhibitor of SARS-CoV-2 main protease (Mpro) and the main ingredient of Paxlovid, a drug approved by the U.S. Food and Drug Administration for high-risk COVID-19 patients. Recently, a rare natural mutation, H172Y, was found to significantly reduce nirmatrelvir's inhibitory activity. As the COVID-19 cases skyrocket in China and the selective pressure of antiviral therapy builds in the US, there is an urgent need to characterize and understand how the H172Y mutation confers drug resistance. Here, we investigated the H172Y Mpro's conformational dynamics, folding stability, catalytic efficiency, and inhibitory activity using all-atom constant pH and fixed-charge molecular dynamics simulations, alchemical and empirical free energy calculations, artificial neural networks, and biochemical experiments. Our data suggest that the mutation significantly weakens the S1 pocket interactions with the N-terminus and perturbs the conformation of the oxyanion loop, leading to a decrease in the thermal stability and catalytic efficiency. Importantly, the perturbed S1 pocket dynamics weaken the nirmatrelvir binding in the P1 position, which explains the decreased inhibitory activity of nirmatrelvir. Our work demonstrates the predictive power of the combined simulation and artificial intelligence approaches, and together with biochemical experiments, they can be used to actively surveil continually emerging mutations of SARS-CoV-2 Mpro and assist the optimization of antiviral drugs. The presented approach, in general, can be applied to characterize mutation effects on any protein drug targets.

Thermal unfolding methods in drug discovery

Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.

The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins

Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.

Towards a Better Understanding of Texturization during High-Moisture Extrusion (HME)-Part I: Modeling the Texturability of Plant-Based Proteins

This study focused on predicting high-moisture texturization of plant-based proteins (soy protein concentrate (SPC), soy protein isolate (SPI), pea protein isolate (PPI)) at different water contents (57.5%, 60%, 65%, 70%, and 72.5% (w/w db)) to optimize and guarantee the production of high-moisture meat analogs (HMMA). Therefore, high-moisture extrusion (HME) experiments were performed, and the texture of the obtained high-moisture extruded samples (HMES) was sensory evaluated and categorized into poorly-textured, textured, or well-textured. In parallel, data on heat capacity (c_p) and phase transition behavior of the plant-based proteins were determined using differential scanning calorimetry (DSC). Based on the DSC data, a model for predicting c_p of hydrated, but not extruded, plant-based proteins was developed. Furthermore, based on the aforementioned model for predicting cp and DSC data on phase transition behavior of the plant-based proteins in combination with conducted HME trials and the mentioned model for predicting cp, a texturization indicator was developed, which could be used to calculate the minimum threshold temperature required to texturize plant-based proteins during HME. The outcome of this study could help to minimize the resources of expensive extrusion trials in the industry to produce HMMA with defined textures.

Investigating Thermally Induced Aggregation of Somatropin- New Insights Using Orthogonal Techniques

Three orthogonal techniques were used to provide new insights into thermally induced aggregation of the therapeutic protein Somatropin at pH 5.8 and 7.0. The techniques were Dynamic Light Scattering (DLS), Asymmetric Flow-Field Flow-Fractionation (AF4), and the TEM-based analysis system MiniTEM™. In addition, Differential Scanning Calorimetry (DSC) was used to study the thermal unfolding and stability. DSC and DLS were used to explain the initial aggregation process and aggregation rate at the two pH values. The results suggest that electrostatic stabilization seems to be the main reason for the faster initial aggregation at pH 5.8, i.e., closer to the isoelectric point of Somatropin. AF4 and MiniTEM were used to investigate the aggregation pathway further. Combining the results allowed us to demonstrate Somatropin's thermal aggregation pathway at pH 7.0. The growth of the aggregates appears to follow two steps. Smaller elongated aggregates are formed in the first step, possibly initiated by partly unfolded species. In the second step, occurring during longer heating, the smaller aggregates assemble into larger aggregates with more complex structures.

Efficient production of the glycosylated derivatives of baicalein in engineered Escherichia coli

Baicalein-7-O-glucoside and baicalein-7-O-rhamnoside have been proven to possess many pharmacological activities and are potential candidate drug leads and herb supplements. However, their further development is largely limited due to low content in host plants. Few studies reported that both bioactive plant components are prepared through the bioconversion of baicalein that is considered as the common biosynthetic precursor of both compounds. Herein, we constructed a series of the engineered whole-cell bioconversion systems in which the deletion of competitive genes and the introduction of exogenous UDP-glucose supply pathway, glucosyltransferase, rhamnosyltransferase, and the UDP-rhamnose synthesis pathway are made. Using these engineered strains, the precursor baicalein is able to be transformed into baicalein-7-O-glucoside and baicalein-7-O-rhamnoside, with high-titer production, respectively. The further optimization of fermentation conditions led to the final production of 568.8 mg/L and 877.0 mg/L for baicalein-7-O-glucoside and baicalein-7-O-rhamnoside, respectively. To the best of our knowledge, it is the highest production in preparation of baicalein-7-O-glucoside from baicalein so far, while the preparation of baicalein-7-O-rhamnoside is the first reported via bioconversion approach. Our study provides a reference for the industrial production of high-value products baicalein-7-O-glucoside and baicalein-7-O-rhamnoside using engineered E. coli. KEY POINTS: • Integrated design for improving the intracellular UDP-glucose pool • High production of rare baicalein glycosides in the engineered E. coli • Baicalein-7-O-glucoside and baicalein-7-O-rhamnoside.

Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14

The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity. Human PEX5 possesses eight of these conserved motifs distributed within its 320-residue disordered N-terminal region. Here, we combine biophysical (ITC, NMR, CD), biochemical and computational methods to characterize the recognition of these (di)aromatic peptides motifs and identify key features that are recognized by PEX14. Notably, the eight motifs present in human PEX5 exhibit distinct affinities and energetic contributions for the interaction with the PEX14 NTD. Computational docking and analysis of the interactions of the (di)aromatic motifs identify the specific amino acids features that stabilize a helical conformation of the peptide ligands and mediate interactions with PEX14 NTD. We propose a refined consensus motif ExWΦxE(F/Y)Φ for high affinity binding to the PEX14 NTD and discuss conservation of the (di)aromatic peptide recognition by PEX14 in other species.

Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry

Flexible in vitro methods alter the course of biological discoveries. Differential Scanning Fluorimetry (DSF) is a particularly versatile technique which reports protein thermal unfolding via fluorogenic dye. However, applications of DSF are limited by widespread protein incompatibilities with the available DSF dyes. Here, we enable DSF applications for 66 of 70 tested proteins (94%) including 10 from the SARS-CoV2 virus using a chemically diverse dye library, Aurora, to identify compatible dye-protein pairs in high throughput. We find that this protein-adaptive DSF platform (paDSF) not only triples the previous protein compatibility, but also fundamentally extends the processes observable by DSF, including interdomain allostery in O-GlcNAc Transferase (OGT). paDSF enables routine measurement of protein stability, dynamics, and ligand binding.

A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion

An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.

Calcium-induced environmental adaptability of the blood protein vitronectin

The adaptability of proteins to their work environments is fundamental for cellular life. Here, we describe how the hemopexin-like domain of the multifunctional blood glycoprotein vitronectin binds Ca2+ to adapt to excursions of temperature and shear stress. Using X-ray crystallography, molecular dynamics simulations, NMR, and differential scanning fluorimetry, we describe how Ca2+ and its flexible hydration shell enable the protein to perform conformational changes that relay beyond the calcium-binding site and alter the number of polar contacts to enhance conformational stability. By means of mutagenesis, we identify key residues that cooperate with Ca2+ to promote protein stability, and we show that calcium association confers protection against shear stress, a property that is advantageous for proteins that circulate in the vasculature, like vitronectin.

Stability profile of the neuronal SNARE complex reflects its potency to drive fast membrane fusion

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) form the SNARE complex to mediate most fusion events of the secretory pathway. The neuronal SNARE complex is featured by its high stability and half-zippered conformation required for driving robust and fast synaptic exocytosis. However, these two features seem to be thermodynamically mutually exclusive. In this study, we have employed temperature-dependent disassociation assays and single-molecule Förster resonance energy transfer (FRET) experiments to analyze the stability and conformation of the neuronal SNARE complex. We reclassified the amino acids of the SNARE motif into four sub-groups (core, core-side I and II, and non-contact). Our data showed that the core residues predominantly contribute to the complex stability to meet a basal requirement for SNARE-mediated membrane fusion, while the core-side residues exert an unbalanced effect on the N- and C-half bundle stability that determines the half-zippered conformation of the neuronal SNARE complex, which would accommodate essential regulations by complexins and synaptotagmins for fast Ca2+-triggered membrane fusion. Furthermore, our data confirmed a strong coupling of folding energy between the N- and C-half assembly of the neuronal SNARE complex, which rationalizes the strong potency of the half-zippered conformation to conduct robust and fast fusion. Overall, these results uncovered that the stability profile of the neuronal SNARE complex reflects its potency to drive fast and robust membrane fusion. Based on these results, we also developed a new parameter, the stability factor (Fs), to characterize the overall stability of the neuronal SNARE complex and resolved a linear correlation between the stability and inter-residue coulombic interactions of the neuronal SNARE complex, which would help rationally design artificial SNARE complexes and remold functional SNARE complexes with desirable stability.

Oncogenic Mutations in the DNA-Binding Domain of FOXO1 that Disrupt Folding: Quantitative Insights from Experiments and Molecular Simulations

FOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting that the loss of function is due to destabilization of the folded structure. Computational modeling of the effect of mutations on FOXO1 folding was performed using alchemical free energy perturbation (FEP), and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix α3. Although FEP can qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent-accessible surface areas from molecular simulations, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that the atomic detail provided by simulations is important for the accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.

Family 1 glycosyltransferases (GT1, UGTs) are subject to dilution-induced inactivation and low chemo stability toward their own acceptor substrates

Glycosylation reactions are essential but challenging from a conventional chemistry standpoint. Conversely, they are biotechnologically feasible as glycosyltransferases can transfer sugar to an acceptor with perfect regio- and stereo-selectivity, quantitative yields, in a single reaction and under mild conditions. Low stability is often alleged to be a limitation to the biotechnological application of glycosyltransferases. Here we show that these enzymes are not necessarily intrinsically unstable, but that they present both dilution-induced inactivation and low chemostability towards their own acceptor substrates, and that these two phenomena are synergistic. We assessed 18 distinct GT1 enzymes against three unrelated acceptors (apigenin, resveratrol, and scopoletin—respectively a flavone, a stilbene, and a coumarin), resulting in a total of 54 enzymes: substrate pairs. For each pair, we varied catalyst and acceptor concentrations to obtain 16 different reaction conditions. Fifteen of the assayed enzymes (83%) displayed both low chemostability against at least one of the assayed acceptors at submillimolar concentrations, and dilution-induced inactivation. Furthermore, sensitivity to reaction conditions seems to be related to the thermal stability of the enzymes, the three unaffected enzymes having melting temperatures above 55°C, whereas the full enzyme panel ranged from 37.4 to 61.7°C. These results are important for GT1 understanding and engineering, as well as for discovery efforts and biotechnological use.

Some Clues about Enzymes from Psychrophilic Microorganisms

Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.

Identification of Core Allosteric Sites through Temperature- and Nucleus-Invariant Chemical Shift Covariance

Allosteric regulation is essential to control biological function. In addition, allosteric sites offer a promising venue for selective drug targeting. However, accurate mapping of allosteric sites remains challenging since allostery relies on often subtle, yet functionally relevant, structural and dynamical changes. A viable approach proposed to overcome such challenge is the chemical shift covariance analysis (CHESCA). Although CHESCA offers an exhaustive map of allosteric networks, it is critical to define the core allosteric sites to be prioritized in subsequent functional studies or the design of allosteric drugs. Here we propose two new CHESCA-based methodologies, called temperature CHESCA (T-CHESCA) and CLASS-CHESCA, aimed at narrowing down allosteric maps to the core allosteric residues. Both T- and CLASS-CHESCAs rely on the invariance of core inter-residue correlations to changes in the chemical shifts of the active and inactive conformations interconverting in fast exchange. In the T-CHESCA the chemical shifts of such states are modulated through temperature changes, while in the CLASS-CHESCA through variations in the spin-active nuclei involved in pairwise correlations. The T- and CLASS-CHESCAs as well as complete-linkage CHESCA were applied to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC), which serves as a prototypical allosteric switch. Residues consistently identified by the three CHESCA methods were found in previously identified EPAC allosteric core sites. Hence, the T-, CLASS- and CL-CHESCA provide a toolset to establish allosteric site hierarchy and triage allosteric sites to be further analyzed by mutations and functional assays. Furthermore, the core allosteric networks selectively revealed through T- and CLASS-CHESCA are expected to facilitate the mechanistic understanding of disease-related mutations and the design of selective allosteric modulators.

Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops

Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.

The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach

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The TIM barrel is a versatile fold to understand structure-stability relationships.

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A collection of de novo TIM barrels with improved hydrophobic cores was designed.

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DeNovoTIMs are reversible in chemical and thermal unfolding, which is uncommon in TIM barrels.

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Epistatic effects play a central role in DeNovoTIMs stabilization.

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DeNovoTIMs navigate a previously uncharted region of the stability landscape.

The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. Understanding and manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (β/⍺)₈-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.

The effects of intramolecular and intermolecular electrostatic repulsions on the stability and aggregation of NISTmAb revealed by HDX-MS, DSC, and nanoDSF

The stability and aggregation of NIST monoclonal antibody (NISTmAb) were investigated by hydrogen/deuterium exchange mass spectrometry (HDX-MS), differential scanning calorimetry (DSC), and nano-differential scanning fluorimetry (nanoDSF). NISTmAb was prepared in eight formulations at four different pHs (pH 5, 6, 7, and 8) in the presence and absence of 150 mM NaCl and analyzed by the three methods. The HDX-MS results showed that NISTmAb is more conformationally stable at a pH near its isoelectric point (pI) in the presence of NaCl than a pH far from its pI in the absence of NaCl. The stabilization effects were global and not localized. The midpoint temperature of protein thermal unfolding transition results also showed the C_H 2 domain of the protein is more conformationally stable at a pH near its pI. On the other hand, the onset of aggregation temperature results showed that NISTmAb is less prone to aggregate at a pH far from its pI, particularly in the absence of NaCl. These seemingly contradicting results, higher conformational stability yet higher aggregation propensity near the pI than far away from the pI, can be explained by intramolecular and intermolecular electrostatic repulsion using Lumry-Eyring model, which separates folding/unfolding equilibrium and aggregation event. The further a pH from the pI, the higher the net charge of the protein. The higher net charge leads to greater intramolecular and intermolecular electrostatic repulsions. The greater intramolecular electrostatic repulsion destabilizes the protein and the greater intermolecular electrostatic repulsion prevents aggregation of the protein molecules at pH far from the pI.

Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator

Cystic Fibrosis (CF) is caused by mutations to the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel. CFTR is composed of two membrane spanning domains, two cytosolic nucleotide-binding domains (NBD1 and NBD2) and a largely unstructured R-domain. Multiple CF-causing mutations reside in the NBDs and some are known to compromise the stability of these domains. The ability to predict the effect of mutations on the stability of the cytosolic domains of CFTR and to shed light on the mechanisms by which they exert their effect is therefore important in CF research. With this in mind, we have predicted the effect on domain stability of 59 mutations in NBD1 and NBD2 using 15 different algorithms and evaluated their performances via comparison to experimental data using several metrics including the correct classification rate (CCR), and the squared Pearson correlation (R²) and Spearman's correlation (ρ) calculated between the experimental ΔT_m values and the computationally predicted ΔΔG values. Overall, the best results were obtained with FoldX and Rosetta. For NBD1 (35 mutations), FoldX provided R² and ρ values of 0.64 and -0.71, respectively, with an 86% correct classification rate (CCR). For NBD2 (24 mutations), FoldX R², ρ, and CCR were 0.51, -0.73, and 75%, respectively. Application of the Rosetta high-resolution protocol (Rosetta_hrp) to NBD1 yielded R², ρ, and CCR of 0.64, -0.75, and 69%, respectively, and for NBD2 yielded R², ρ, and CCR of 0.29, -0.27, and 50%, respectively. The corresponding numbers for the Rosetta's low-resolution protocol (Rosetta_lrp) were R² = 0.47, ρ = -0.69, and CCR = 69% for NBD1 and R² = 0.27, ρ = -0.24, and CCR = 63% for NBD2. For NBD1, both algorithms suggest that destabilizing mutations suffer from destabilizing vdW clashes, whereas stabilizing mutations benefit from favorable H-bond interactions. Two triple consensus approaches based on FoldX, Rosetta_lpr, and Rosetta_hpr were attempted using either "majority-voting" or "all-voting". The all-voting consensus outperformed the individual predictors, albeit on a smaller data set. In summary, our results suggest that the effect of mutations on the stability of CFTR's NBDs could be largely predicted. Since NBDs are common to all ABC transporters, these results may find use in predicting the effect and mechanism of the action of multiple disease-causing mutations in other proteins.

Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA

Molecular basis of protein stability at different temperatures is a fundamental problem in protein science that is substantially far from being accurately and quantitatively solved as it requires an explicit knowledge of the temperature dependence of folding free energy of amino acid residues. In the present study, we attempted to gain insights into the thermodynamic stability of SazCA and its implications on protein folding/unfolding. We report molecular dynamics simulations of water solvated SazCA in a temperature range of 293-393 K to study the relationship between the thermostability and flexibility. Our structural analysis shows that the protein maintains the highest structural stability at 353 K and the protein conformations are highly flexible at temperatures above 353 K. Larger exposure of hydrophobic surface residues to the solvent medium for conformations beyond 353 K were identified from H-bond analysis. Higher number of secondary structure contents exhibited by SazCA at 353 K corroborated the conformations at 353 K to exhibit the highest thermal stability. The analysis of thermodynamics of protein stability revealed that the conformations that denature at higher melting temperatures tend to have greater maximum thermal stability. Our analysis shows that 353 K conformations have the highest melting temperature, which was found to be close to the experimental optimum temperature. The enhanced protein stability at 353 K due the least value of heat capacity at unfolding suggested an increase in folding. Comparative Gibbs free energy analysis and funnel shaped energy landscape confirmed a transition in folding/unfolding pathway of SazCA at 353 K.

Three Simple Properties Explain Protein Stability Change upon Mutation

Accurate prediction of protein stability upon mutation enables rational engineering of new proteins and insights into protein evolution and monogenetic diseases caused by single-point amino acid substitutions. Many tools have been developed to this aim, ranging from energy-based models to machine-learning methods that use large amounts of experimental data. However, as the methods become more complex, the interpretation of the chemistry underlying the protein stability effects becomes obscure. It is thus of interest to identify the simplest prediction model that retains complete amino acid specific interpretation; for a given number of input descriptors, we expect such a model to be almost universal. In this study, we identify such a limiting model, SimBa, a simple multilinear regression model trained on a substitution-type-balanced experimental data set. The model accounts only for the solvent accessibility of the site, volume difference, and polarity difference caused by mutation. Our results show that this very simple and directly applicable model performs comparably to other much more complex, widely used protein stability prediction methods. This suggests that a hard limit of ∼1 kcal/mol numerical accuracy and an R ∼ 0.5 trend accuracy exists and that new features, such as account of unfolded states, water colocalization, and amino acid correlations, are required to improve accuracy to, e.g., 1/2 kcal/mol.

Effect of Met/Leu substitutions on the stability of NAD+-dependent formate dehydrogenases from Gossypium hirsutum

NAD⁺-dependent formate dehydrogenases (FDHs) are extensively used in the regeneration of NAD(P)H and the reduction of CO₂ to formate. In addition to their industrial importance, FDHs also play a crucial role in the maintenance of a reducing environment to combat oxidative stress in plants. Therefore, it is important to investigate the response of NAD⁺-dependent FDH against both temperature and H₂O₂, to understand the defense mechanisms, and to increase its stability under oxidative stress conditions. In the present study, we characterized the oxidative and thermal stability of NAD⁺-dependent FDH isolated from cotton, Gossypium hirsutum (GhFDH), by investigating the effect of Met/Leu substitutions in the positions of 225, 234, and 243. Results showed that the single mutant, M234L (0.72 s^-1 mM^-1), and the triple mutant, M225L/M234L/M243L (0.55 s^-1 mM^-1), have higher catalytic efficiency than the native enzyme. Substitution of methionine by leucine on the position of 243 increased the free energy gain by 670 J mol^-1. The most remarkable results in chemical stability were seen for double and triple mutants, cumulatively. Double and triple substitution of Met to Leu (M225L/M243L and M225L/M243L/M234L) reduce the k^ef_in by a factor of 2 (12.3×10^-5 and 12.8×10^-5 s^-1, respectively.Key points• The closer the residue to NAD⁺, in which we substituted methionine to leucine, the lower the stability against H₂O₂ we observed.• The significant gain in the T_m value for the M243L mutant was observed as +5°C.• Residue 234 occupies a critical position for oxidation defense mechanisms. Graphical abstract (a) Methionine amino acids on the protein surface are susceptible to oxidative stress and can be converted to methionine sulfoxide by reactive oxygen derivatives (such as hydrogen peroxide). Therefore, they are critical regions in the change of protein conformation and loss of activity. (b) Replacing the amino acid methionine, which is susceptible to oxidation due to the sulfur group, with the oxidation-resistant leucine amino acid is an important strategy in increasing oxidative stability.

Label-Free Target Identification and Confirmation Using Thermal Stability Shift Assays

Target identification presents one of the biggest challenges to chemical genomic approaches. In recent years, several methods have been applied for target identification and validation in plant cells. Here, we describe a label-free method based on the thermodynamic stabilization of a protein by interaction with a small-molecule ligand. With increasing temperature, proteins undergo thermal denaturation resulting in irreversible aggregation and precipitation. The binding of a small molecule to its target can enhance protein stability resulting in an increased temperature of aggregation (T_agg). This distinct increase in the temperature of aggregation known as a thermal shift can identify a compound-target protein interaction in high-throughput assays or, validate a predicted interaction.

Why small proteins tend to have high denaturation temperatures

Data indicate that small globular proteins (consisting of less than about 70 residues) tend to have high denaturation temperatures. This finding is analysed by comparing experimental denaturation enthalpy and entropy changes of a selected set of small proteins with values calculated on the basis of average and common properties of globular proteins. The conclusion is that the denaturation entropy change is smaller than expected, leading to an increase in denaturation temperature. The proposed molecular rationalization considers the existence of long-wavelength, low-frequency vibrational modes in the native state of small proteins due to their large surface-to-interior ratio. The effect of decreasing the conformational entropy gain associated with denaturation on thermal stability is directly verified by means of an already devised theoretical model [G. Graziano, Phys. Chem. Chem. Phys. 2010, 12, 14245-14252; 2014, 16, 21755-21767].

Common mechanism of thermostability in small α- and β-proteins studied by molecular dynamics

Protein thermostability is important to evolution, diseases, and industrial applications. Proteins use diverse molecular strategies to achieve stability at high temperature, yet reducing the entropy of unfolding seems required. We investigated five small α-proteins and five β-proteins with known, distinct structures and thermostability (T_m ) using multi-seed molecular dynamics simulations at 300, 350, and 400 K. The proteins displayed diverse changes in hydrogen bonding, solvent exposure, and secondary structure with no simple relationship to T_m . Our dynamics were in good agreement with experimental B-factors at 300 K and insensitive to force-field choice. Despite the very distinct structures, the native-state (300 + 350 K) free-energy landscapes (FELs) were significantly broader for the two most thermostable proteins and smallest for the three least stable proteins in both the α- and β-group and with both force fields studied independently (tailed t-test, 95% confidence level). Our results suggest that entropic ensembles stabilize proteins at high temperature due to reduced entropy of unfolding, viz., ΔG = ΔH - TΔS. Supporting this mechanism, the most thermostable proteins were also the least kinetically stable, consistent with broader FELs, typified by villin headpiece and confirmed by specific comparison to a mesophilic ortholog of Thermus thermophilus apo-pyrophosphate phosphohydrolase. We propose that molecular strategies of protein thermostabilization, although diverse, tend to converge toward highest possible entropy in the native state consistent with the functional requirements. We speculate that this tendency may explain why many proteins are not optimally structured and why molten-globule states resemble native proteins so much.

Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins

The protein misfolding avoidance hypothesis explains the universal negative correlation between protein abundance and sequence evolutionary rate across the proteome by identifying protein folding free energy (ΔG) as the confounding variable. Abundant proteins resist toxic misfolding events by being more stable, and more stable proteins evolve slower because their mutations are more destabilizing. Direct supporting evidence consists only of computer simulations. A study taking advantage of a recent experimental breakthrough in measuring protein stability proteome-wide through melting temperature (Tm) (Leuenberger et al. 2017), found weak misfolding avoidance hypothesis support for the Escherichia coli proteome, and no support for the Saccharomyces cerevisiae, Homo sapiens, and Thermus thermophilus proteomes (Plata and Vitkup 2018). I find that the nontrivial relationship between Tm and ΔG and inaccuracy in Tm measurements by Leuenberger et al. 2017 can be responsible for not observing strong positive abundance-Tm and strong negative Tm-evolutionary rate correlations.

Limits to Compensatory Mutations: Insights from Temperature-Sensitive Alleles

Previous experiments with temperature-sensitive mutants of the yeast enzyme orotidine 5'-phosphate decarboxylase (encoded in gene URA3) yielded the unexpected result that reversion occurs only through exact reversal of the original mutation (Jakubowska A, Korona R. 2009. Lack of evolutionary conservation at positions important for thermal stability in the yeast ODCase protein. Mol Biol Evol. 26(7):1431-1434.). We recreated a set of these mutations in which the codon had two nucleotide substitutions, making exact reversion much less likely. We screened these double mutants for reversion and obtained a number of compensatory mutations occurring at alternative sites in the molecule. None of these compensatory mutations fully restored protein performance. The mechanism of partial compensation is consistent with a model in which protein stabilization is additive, as the same secondary mutations can compensate different primary alternations. The distance between primary and compensatory residues precludes direct interaction between the sites. Instead, most of the compensatory mutants were clustered in proximity to the catalytic center. All of the second-site compensatory substitutions occurred at relatively conserved sites, and the amino acid replacements were to residues found at these sites in a multispecies alignment of the protein. Based on the estimated distribution of changes in Gibbs free energy among a large number of amino acid replacements, we estimate that, for most proteins, the probability that a second-site mutation would have a sufficiently large stabilizing effect to offset a temperature-sensitive mutation in the order of 10-4 or less. Hence compensation is likely to take place only for slightly destabilizing mutations because highly stabilizing mutations are exceeding rare.

Dodine as a Kosmo-Chaotropic Agent

Denaturants such as the guanidinium cation unfold proteins at molar concentrations, which interferes with ultraviolet- and infrared-based spectroscopy measurements. Dodine denatures some proteins cooperatively at a thousand-fold lower concentration, allowing for spectroscopy measurements. Nonetheless, dodine's microscopic mechanism of interaction with proteins is not understood. We probe the effect of dodine on α-helices and tertiary structure by investigating the stability of the small helical protein B. Experiments show that dodine promotes formation of helical structure (a kosmotropic effect), while inducing the loss of tertiary structure (a chaotropic effect). Although dodine destabilizes native protein structure, it does not lower the thermal denaturation midpoint temperature of protein B. All-atom simulations reveal the cause for both observations: The denaturant action of dodine's guanidyl headgroup is counteracted by its aliphatic tail, which stabilizes amphipathic helices and associates with an expanded protein core. The Janus-like behavior of headgroup and tail make dodine a simultaneous stabilizer-destabilizer or "kosmo-chaotrope".

Genetic code ambiguity modulates the activity of a C. albicans MAP kinase linked to cell wall remodeling

The human fungal pathogen Candida albicans ambiguously decodes the universal leucine CUG codon predominantly as serine but also as leucine. C. albicans has a high capacity to survive and proliferate in adverse environments but the rate of leucine incorporation fluctuates in response to different stress conditions. C. albicans is adapted to tolerate this ambiguous translation through a mechanism that combines drastic decrease in CUG usage and reduction of CUG-encoded residues in conserved positions in the protein sequences. However, in a few proteins, the residues encoded by CUG codons are found in strictly conserved positions, suggesting that this genetic code alteration might have a functional impact. One such example is Cek1, a central signaling protein kinase that contains a single CUG-encoded residue at a conserved position, whose identity might regulate the correct flow of information across the MAPK cascade. Here we show that insertion of a leucine at the CUG-encoded position decreases the stability of Cek1, apparently without major structural alterations. In contrast, incorporation of a serine residue at the CUG position induces the autophosphorylation of the conserved tyrosine residue of the Cek1 ²³¹TEY²³³ motif, and increases its intrinsic kinase activity in vitro. These findings show that CUG ambiguity modulates the activity of Cek1, a key kinase directly linked to morphogenesis and virulence in C. albicans.

Ensemble Properties of Bax Determine Its Function

BAX and BAK are essential mediators of intrinsic apoptosis that permeabilize the mitochondrial outer membrane. BAX activation requires its translocation from cytosol to mitochondria where conformational changes cause its oligomerization. To better understand the critical step of translocation, we examined its blockade by mutation near the C terminus (P168G) or by antibody binding near the N terminus. Similarities in the crystal structures of wild-type and BAX P168G but significant other differences suggest that cytosolic BAX exists as an ensemble of conformers, and that the distribution of conformers within the ensemble determines the different functions of wild-type and mutant proteins. We also describe the structure of BAX in complex with an antibody, 3C10, that inhibits cytosolic BAX by limiting exposure of the membrane-associating helix α9, as does the P168G mutation. Our data for both means of BAX inhibition argue for an allosteric model of BAX regulation that derives from properties of the ensemble of conformers.

The Analysis of Variants in the General Population Reveals That PMM2 Is Extremely Tolerant to Missense Mutations and That Diagnosis of PMM2-CDG Can Benefit from the Identification of Modifiers

Type I disorders of glycosylation (CDG), the most frequent of which is phosphomannomutase 2 (PMM2-CDG), are a group of diseases causing the incomplete N-glycosylation of proteins. PMM2-CDG is an autosomal recessive disease with a large phenotypic spectrum, and is associated with mutations in the PMM2 gene. The biochemical analysis of mutants does not allow a precise genotype⁻phenotype correlation for PMM2-CDG. PMM2 is very tolerant to missense and loss of function mutations, suggesting that a partial deficiency of activity might be beneficial under certain circumstances. The patient phenotype might be influenced by variants in other genes associated with the type I disorders of glycosylation in the general population.

Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection

Substrate binding proteins represent a large protein family that plays fundamental roles in selective transportation of metabolites across membrane. The function of these proteins relies on the relative motions of their two domains. Insights into domain communication in this class of proteins have been here collected using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model system. TmArgBP was dissected into two domains (D1 and D2) that were exhaustively characterized using a repertoire of different experimental and computational techniques. Indeed, stability, crystalline structure, ability to recognize the arginine substrate, and dynamics of the two individual domains have been here studied. Present data demonstrate that, although in the parent protein both D1 and D2 cooperate for the arginine anchoring; only D1 is intrinsically able to bind the substrate. The implications of this finding on the mechanism of arginine binding and release by TmArgBP have been discussed. Interestingly, both D1 and D2 retain the remarkable thermal/chemical stability of the parent protein. The analysis of the structural and dynamic properties of TmArgBP and of the individual domains highlights possible routes of domain communication. Finally, this study generated two interesting molecular tools, the two stable isolated domains that could be used in future investigations.

The Effects of One Amino Acid Substitutions at the C-Terminal Region of Thermostable L2 Lipase by Computational and Experimental Approach

The substitutions of the amino acid at the predetermined critical point at the C-terminal of L2 lipase may increase its thermostability and enzymatic activity, or even otherwise speed up the unfolding of the protein structure. The C-terminal of most proteins is often flexible and disordered. However, some protein functions are directly related to flexibility and play significant role in enzyme reaction. The critical point for mutation of L2 lipase structure was predicted at the position 385 of the L2 sequence, and the best three mutants were determined based on I-Mutant2.0 software. The best three mutants were S385E, S385I and S385V. The effects of the substitution of the amino acids at the critical point were analysed with molecular dynamics simulation by using Yet Another Scientific Artificial Reality Application software. The predicted mutant L2 lipases were found to have lower root mean square deviation value as compared to L2 lipase. It was indicated that all the three mutants had higher compactness in the structure, consequently enhanced the stability. Root mean square fluctuation analysis showed that the flexibility of L2 lipase was reduced by mutations. Purified S385E lipase had an optimum temperature of 80 °C in Tris-HCl pH 8. The highest enzymatic activity of purified S385E lipase was obtained at 80 °C temperature in Tris-HCl pH 8, while for L2 lipase it was at 70 °C in Glycine-NaOH pH 9. The thermal stability of S385V lipase was enhanced as compared to other protein since that the melting point (T _m) value was at 85.96 °C. S385I lipase was more thermostable compared to recombinant L2 lipase and other mutants at temperature 60 °C within 16 h preincubation.

Localized conformational changes trigger the pH-induced fibrillogenesis of an amyloidogenic λ light chain protein

Solvent conditions modulate the expression of the amyloidogenic potential of proteins. In this work the effect of pH on the fibrillogenic behavior and the conformational properties of 6aJL2, a model protein of the highly amyloidogenic variable light chain λ6a gene segment, was examined. Ordered aggregates showing the ultrastructural and spectroscopic properties observed in amyloid fibrils were formed in the 2.0-8.0 pH range. At pH <3.0 a drastic decrease in lag time and an increase in fibril formation rate were found. In the 4.0-8.0 pH range there was no spectroscopic evidence for significant conformational changes in the native state. Likewise, heat capacity measurements showed no evidence for residual structure in the unfolded state. However, at pH <3.0 stability is severely decreased and the protein suffers conformational changes as detected by circular dichroism, tryptophan and ANS fluorescence, as well as by NMR spectroscopy. Molecular dynamics simulations indicate that acid-induced conformational changes involve the exposure of the loop connecting strands E and F. These results are compatible with pH-induced changes in the NMR spectra. Overall, the results indicate that the mechanism involved in the acid-induced increase in the fibrillogenic potential of 6aJL2 is profoundly different to that observed in κ light chains, and is promoted by localized conformational changes in a region of the protein that was previously not known to be involved in acid-induced light chain fibril formation. The identification of this region opens the potential for the design of specific inhibitors.

Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations

Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree of sequence conservation makes Trx very amenable to ancestral protein reconstruction techniques. In this work, we address the study of the structural and energetic determinants of thermostability in E. coli Trx using a dataset of mutations inspired by ancestral reconstruction. We compute, from first principles, the expected contribution of 19 different amino acid substitutions to the stability (ΔΔG) and the melting temperature (ΔT_m) of the protein. We also describe the specific changes in structure and protein dynamics responsible for the stabilizing or destabilizing effects of these mutations. Our results point to local and independent changes for most of the variants. Our predictions are accurate enough to substantiate the proposal of new hypotheses regarding evolutionary relationships between mutations, as in the case of T89R, P68A and G74S or K90L and F102A, and reach beyond the initial set to suggest improved variants, such as K90I or K90Y.

Comment on “Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors” by A. Battisti, G. Ciasca, A. Grottesi and A. Tenenbaum, Phys. Chem. Chem. Phys., 2017, 19, 8435

Chain compaction is favoured on raising the temperature because the entropy gain of water molecules due to the decrease in solvent-excluded volume increases with temperature.

Free energy calculations on the stability of the 14-3-3ζ protein

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.

Mutation of Asn-475 in the Venezuelan Equine Encephalitis Virus nsP2 Cysteine Protease Leads to a Self-Inhibited State

The alphaviral nsP2 cysteine protease of the Venezuelan equine encephalitis virus (VEEV) is a validated antiviral drug target. Clan CN proteases contain a cysteine protease domain that is intimately packed with an S-adenosyl-l-methionine-dependent RNA methyltransferase (SAM MTase) domain. Within a cleft formed at the interface of these two domains, the peptide substrate is thought to bind. The nucleophilic cysteine can be found within a conserved motif, ⁴⁷⁵NVCWAK⁴⁸⁰, which differs from that of papain (²²CGSCWAFS²⁹). Mutation of the motif residue, N475, to alanine unexpectedly produced a self-inhibited state in which the N-terminal residues flipped into the substrate-binding cleft. Notably, the N-terminal segment was not hydrolyzed-consistent with a catalytically incompetent state. The N475A mutation resulted in a 70-fold decrease in k_cat/K_m. A side chain-substrate interaction was predicted by the structure; the S701A mutation led to a 17-fold increase in K_m. An Asn at the n-2 position relative to the Cys was also found in the coronaviral papain-like proteases/deubiquitinases (PLpro) of the SARS and MERS viruses, and in several papain-like human ubiquitin specific proteases (USP). The large conformational change in the N475A variant suggests that Asn-475 plays an important role in stabilizing the N-terminal residues and in orienting the carbonyl during nucleophilic attack but does not directly hydrogen bond the oxyanion. The state trapped in crystallo is an unusual result of site-directed mutagenesis but reveals the role of this highly conserved Asn and identifies key substrate-binding contacts that may be exploited by peptide-like inhibitors.