Graded Structural Polymorphism in a Bacterial Thermosensor Protein

YmoA functions as a molecular stress sensor in Yersinia

Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signals through YmoA remain elusive. Our study employs nuclear magnetic resonance spectroscopy, biological assays and RNA-seq analysis to elucidate these mechanisms. We demonstrate that YmoA undergoes structural fluctuations and conformational dynamics in response to temperature and osmolarity changes, correlating with changes in plasmid copy number, bacterial fitness and virulence function. Notably, chemical shift analysis identifies key roles of a few specific residues and of the C-terminus region in sensing both temperature and salt-driven switch. These findings demonstrate that YmoA acts as a central stress sensor in Yersinia, fine-tuning virulence gene expression and balancing metabolic trade-offs.

Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS

Environmentally regulated gene expression is critical for bacterial survival under stress conditions, including extremes in temperature, osmolarity and nutrient availability. Here, we dissect the thermo- and osmo-responsory behavior of the transcriptional repressor H-NS, an archetypal nucleoid-condensing sensory protein, ubiquitous in enterobacteria that infect the mammalian gut. Through experiments and thermodynamic modeling, we show that H-NS exhibits osmolarity, temperature and concentration dependent self-association, with a highly polydisperse native ensemble dominated by monomers, dimers, tetramers and octamers. The relative population of these oligomeric states is determined by an interplay between dimerization and higher-order oligomerization, which in turn drives a competition between weak homo- versus hetero-oligomerization of protein-protein and protein-DNA complexes. A phosphomimetic mutation, Y61E, fully eliminates higher-order self-assembly and preserves only dimerization while weakening DNA binding, highlighting that oligomerization is a prerequisite for strong DNA binding. We further demonstrate the presence of long-distance thermodynamic connectivity between dimerization and oligomerization sites on H-NS which influences the binding of the co-repressor Cnu, and switches the DNA binding mode of the hetero-oligomeric H-NS:Cnu complex. Our work thus uncovers important organizational principles in H-NS including a multi-layered thermodynamic control, and provides a molecular framework broadly applicable to other thermo-osmo sensory proteins that employ similar mechanisms to regulate gene expression.

Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins

Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.

Salmonella spp. in low water activity food: Occurrence, survival mechanisms, and thermoresistance

The occurrence of disease outbreaks involving low-water-activity (a_w ) foods has gained increased prominence due in part to the fact that reducing free water in these foods is normally a measure that controls the growth and multiplication of pathogenic microorganisms. Salmonella, one of the main bacteria involved in these outbreaks, represents a major public health problem worldwide and in Brazil, which highlights the importance of good manufacturing and handling practices for food quality. The virulence of this pathogen, associated with its high ability to persist in the environment, makes Salmonella one of the main challenges for the food industry. The objectives of this article are to present the general characteristics, virulence, thermoresistance, control, and relevance of Salmonella in foodborne diseases, and describe the so-called low-water-activity foods and the salmonellosis outbreaks involving them.

Heterogeneity in Protein Folding and Unfolding Reactions

Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.

Predicting and Simulating Mutational Effects on Protein Folding Kinetics

Mutational perturbations of protein structures, i.e., phi-value analysis, are commonly employed to probe the extent of involvement of a particular residue in the rate-determining step(s) of folding. This generally involves the measurement of folding thermodynamic parameters and kinetic rate constants for the wild-type and mutant proteins. While computational approaches have been reasonably successful in understanding and predicting the effect of mutations on folding thermodynamics, it has been challenging to explore the same on kinetics due to confounding structural, energetic, and dynamic factors. Accordingly, the frequent observation of fractional phi-values (mean of ~0.3) has resisted a precise and consistent interpretation. Here, we describe how to construct, parameterize, and employ a simple one-dimensional free energy surface model that is grounded in the basic tenets of the energy landscape theory to predict and simulate the effect of mutations on folding kinetics. As a proof of principle, we simulate one-dimensional free energy profiles of 806 mutations from 24 different proteins employing just the experimental destabilization as input, reproduce the relative unfolding activation free energies with a correlation of 0.91, and show that the mean phi-value of 0.3 essentially corresponds to the extent of stabilization energy gained at the barrier top while folding.

Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

Single domain proteins fold via diverse mechanisms emphasizing the intricate relationship between energetics and structure, which is a direct consequence of functional constraints and demands imposed at the level of sequence. On the other hand, elucidating the interplay between folding mechanisms and function is challenging in large proteins, given the inherent shortcomings in identifying metastable states experimentally and the sampling limitations associated with computational methods. Here, we show that free energy profiles and surfaces of large systems (>150 residues), as predicted by a statistical mechanical model, display a wide array of folding mechanisms with ubiquitous folding intermediates and heterogeneous native ensembles. Importantly, residues around the ligand binding or enzyme active site display a larger tendency to partially unfold and this manifests as intermediates or excited states along the folding coordinate in ligand binding domains, transcription repressors, and representative enzymes from all the six classes, including the SARS-CoV-2 receptor binding domain (RBD) of the spike protein and the protease M^pro. It thus appears that it is relatively easier to distill the imprints of function on the folding landscape of larger proteins as opposed to smaller systems. We discuss how an understanding of energetic-entropic features in ordered proteins can pinpoint specific avenues through which folding mechanisms, populations of partially structured states and function can be engineered.

A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures

Protein sequences and structures evolve by satisfying varied physical and biochemical constraints. This multi-level selection is enabled not just by the patterning of amino acids on the sequence, but also via coupling between residues in the native structure. Here, we employ an energetically detailed statistical mechanical model with millions of microstates to extract such long-range structural correlations, i.e. thermodynamic coupling free energies, from a diverse family of protein structures. We find that despite the intricate and anisotropic distribution of coupling patterns, the majority of residues (>70%) are only marginally coupled contributing to functional motions and catalysis. Physical origins of ‘sectors’, determinants of native ensemble heterogeneity in extant, ancient and designed proteins, and the basis for allostery emerge naturally from coupling free energies. The statistical framework highlights how evolutionary selection and optimization occur at the level of global interaction network for a given protein fold impacting folding, function, and allosteric outputs.

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Evolution of protein structures occurs at the level of global interaction network.

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More than 70% of the protein residues are weakly or marginally coupled.

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Functional ‘sector’ regions are a manifestation of marginal coupling.

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Coupling indices vary across the entire proteins in extant-ancient and natural-designed pairs.

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The proposed methodology can be used to understand allostery and epistasis.

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains

Native states of folded proteins are characterized by a large ensemble of conformations whose relative populations and interconversion dynamics determine the functional output. This is more apparent in transcription factors that have evolved to be inherently sensitive to small perturbations, thus fine-tuning gene expression. To explore the extent to which such functional features are imprinted on the folding landscape of transcription factor ligand-binding domains (LBDs), we characterize paralogous LBDs of the nuclear receptor (NR) family employing an energetically detailed and ensemble-based Ising-like statistical mechanical model. We find that the native ensembles of the LBDs from glucocorticoid receptor, PPAγ, and thyroid hormone receptor display a remarkable diversity in the width of the native wells, the number and nature of partially structured states, and hence the degree of conformational order. Monte Carlo simulations employing the full state representation of the ensemble highlight that many of the functional conformations coexist in equilibrium, whose relative populations are sensitive to both temperature and the strength of ligand binding. Allosteric modulation of the degree of structure at a coregulator binding site on ligand binding is shown to arise via a redistribution of populations in the native ensembles of glucocorticoid and PPAγ LBDs. Our results illustrate how functional requirements can drive the evolution of conformationally diverse native ensembles in paralogs.

A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble

The high flexibility of long disordered or partially structured loops in folded proteins allows for entropic stabilization of native ensembles. Destabilization of such loops could alter the native ensemble or promote alternate conformations within the native ensemble if the ordered regions themselves are held together weakly. This is particularly true of downhill folding systems that exhibit weak unfolding cooperativity. Here, we combine experimental and computational methods to probe the response of the native ensemble of a helical, downhill folding domain PDD, which harbors an 11-residue partially structured loop, to perturbations. Statistical mechanical modeling points to continuous structural changes on both temperature and mutational perturbations driven by entropic stabilization of partially structured conformations within the native ensemble. Long time-scale simulations of the wild-type protein and two mutants showcase a remarkable conformational switching behavior wherein the parallel helices in the wild-type protein sample an antiparallel orientation in the mutants, with the C-terminal helix and the loop connecting the helices displaying high flexibility, disorder, and non-native interactions. We validate these computational predictions via the anomalous fluorescence of a native tyrosine located at the interface of the helices. Our observations highlight the role of long loops in determining the unfolding mechanisms, sensitivity of the native ensembles to mutational perturbations and provide experimentally testable predictions that can be explored in even two-state folding systems.

Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis

Slow polypeptide conformational changes on time scales of >1 s are generally assumed to be highly cooperative two-state transitions, reflecting the high energy barrier. However, few experimental characterizations have tested the validity of this assumption. We performed residue-specific NMR thermodynamic analysis of the 27-residue lantibiotic peptide, nukacin ISK-1, to characterize the isomerization between two topological states on the second time scale. Unexpectedly, the thermal transition behaviors were distinct among peptide regions, indicating that the topological isomerization process is a mosaic of different degrees of cooperativity. The conformational change path between the two NMR structures was deduced by a targeted molecular dynamics simulation. The unique side-chain threading motions through the monosulfide rings are the structural basis of the high energy barrier, and the nonlocal interactions in the hydrophobic core are the structural basis of the cooperativity. Taken together, we provide an energetic description of the topological isomerization of nukacin ISK-1.

Thermodynamics and folding landscapes of large proteins from a statistical mechanical model

Statistical mechanical models that afford an intermediate resolution between macroscopic chemical models and all-atom simulations have been successful in capturing folding behaviors of many small single-domain proteins. However, the applicability of one such successful approach, the Wako-Saitô-Muñoz-Eaton (WSME) model, is limited by the size of the protein as the number of conformations grows exponentially with protein length. In this work, we surmount this size limitation by introducing a novel approximation that treats stretches of 3 or 4 residues as blocks, thus reducing the phase space by nearly three orders of magnitude. The performance of the 'bWSME' model is validated by comparing the predictions for a globular enzyme (RNase H) and a repeat protein (IκBα), against experimental observables and the model without block approximation. Finally, as a proof of concept, we predict the free-energy surface of the 370-residue, multi-domain maltose binding protein and identify an intermediate in good agreement with single-molecule force-spectroscopy measurements. The bWSME model can thus be employed as a quantitative predictive tool to explore the conformational landscapes of large proteins, extract the structural features of putative intermediates, identify parallel folding paths, and thus aid in the interpretation of both ensemble and single-molecule experiments.

Thermally versus Chemically Denatured Protein States

Protein unfolding thermodynamic parameters are conventionally extracted from equilibrium thermal and chemical denaturation experiments. Despite decades of work, the degree of structure and the compactness of denatured states populated in these experiments are still open questions. Here, building on previous works, we show that thermally and chemically denatured protein states are distinct from the viewpoint of far-ultraviolet circular dichroism experiments that report on the local conformational status of peptide bonds. The differences identified are independent of protein length, structural class, or experimental conditions, highlighting the presence of two sub-ensembles within the denatured states. The sub-ensembles, U_T and U_D for thermally induced and denaturant-induced unfolded states, respectively, can exclusively exchange populations as a function of temperature at high chemical denaturant concentrations. Empirical analysis suggests that chemically denatured states are ∼50% more expanded than the thermally denatured chains of the same protein. Our observations hint that the strength of protein backbone-backbone interactions and identity versus backbone-solvent/co-solvent interactions determine the conformational distributions. We discuss the implications for protein folding mechanisms, the heterogeneity in relaxation rates, and folding diffusion coefficients.

A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair

Uropathogenic E. coli experience a wide range of osmolarity conditions before and after successful infection. Stress-responsive regulatory proteins in bacteria, particularly proteins of the Hha family and H-NS, a transcription repressor, sense such osmolarity changes and regulate transcription through unknown mechanisms. Here we use an array of experimental probes complemented by molecular simulations to show that Cnu, a member of the Hha protein family, acts as an exquisite molecular sensor of solvent ionic strength. The osmosensory behavior of Cnu involves a fine-tuned modulation of disorder in the fourth helix and the three-dimensional structure in a graded manner. Order-disorder transitions in H-NS act synergistically with molecular swelling of Cnu contributing to a salt-driven switch in binding cooperativity. Thus, sensitivity to ambient conditions can be imprinted at the molecular level by tuning not just the degree of order in the protein conformational ensemble but also through population redistributions of higher-order molecular complexes.

The bacterial protein Cnu together with the transcription repressor H-NS regulate expression of virulence factors in an osmo-sensitive manner. Here authors show that the structure of Cnu swells with decreasing ionic strength driving the oligomerization of H-NS and regulating osmo-sensory response.

Switching Protein Conformational Substates by Protonation and Mutation

Protein modules that regulate the availability and conformational status of transcription factors determine the rapidity, duration, and magnitude of cellular response to changing conditions. One such system is the single-gene product Cnu, a four-helix bundle transcription co-repressor, which acts as a molecular thermosensor regulating the expression of virulence genes in enterobacteriaceae through modulation of its native conformational ensemble. Cnu and related genes have also been implicated in pH-dependent expression of virulence genes. We hypothesize that protonation of a conserved buried histidine (H45) in Cnu promotes large electrostatic frustration, thus disturbing the H-NS, a transcription factor, binding face. Spectroscopic and calorimetric methods reveal that H45 exhibits a suppressed p K_a of ∼5.1, the protonation of which switches the conformation to an alternate native ensemble in which the fourth helix is disordered. The population redistribution can also be achieved through a mutation H45V, which does not display any switching behavior at pH values greater than 4. The Wako-Saitô-Muñoz-Eaton (WSME) statistical mechanical model predicts specific differences in the conformations and fluctuations of the fourth and first helices of Cnu determining the observed pH response. We validate these predictions through fluorescence lifetime measurements of a sole tryptophan, highlighting the presence of both native and non-native interactions in the regions adjoining the binding face of Cnu. Our combined experimental-computational study thus shows that Cnu acts both as a thermo- and pH-sensor orchestrated via a subtle but quantifiable balance between the weak packing of a structural element and protonation of a buried histidine that promotes electrostatic frustration.

Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition

Using multi-site time-resolved FRET, it is shown that equilibrium unfolding of monellin is not only heterogeneous, but that the degree of non-cooperativity differs between the sole α-helix and different parts of the β-sheet.

Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein

The mesoscale nature of proteins allows for an efficient coupling between environmental cues and conformational changes, enabling their function as molecular transducers. Delineating the precise structural origins of such a connection and the expected spectroscopic response has, however, been challenging. In this work, we perform a combination of urea-temperature double perturbation experiments and theoretical modeling to probe the conformational landscape of Cnu, a natural thermosensor protein. We observe unique ensemble signatures that point to a continuum of conformational substates in the native ensemble and that respond intricately to perturbations upon monitoring secondary and tertiary structures, distances between an intrinsic FRET pair, and hydrodynamic volumes. Binding assays further reveal a weakening of the Cnu functional complex with temperature, highlighting the molecular origins of signal transduction critical for pathogenic response in enterobacteriaceae.