Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery

Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT

The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mMpro monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mMpro shows that the mMpro-PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mMpro monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.

Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble

The functioning of proteins is intimately tied to their fluctuations in the native ensemble. The structural-energetic features that determine fluctuation amplitudes and hence the shape of the underlying landscape, which in turn determine the magnitude of the functional output, are often confounded by multiple variables. Here, we employ the FF1 domain from human p190A RhoGAP protein as a model system to uncover the molecular basis for phosphorylation of a buried tyrosine, which is crucial to the transcriptional activity associated with transcription factor TFII-I. Combining spectroscopy, calorimetry, statistical-mechanical modeling, molecular simulations, and in vitro phosphorylation assays, we show that the FF1 domain samples a diverse array of conformations in its native ensemble, some of which are phosphorylation-competent. Upon eliminating unfavorable charge-charge interactions through a single charge-reversal (K53E) or charge-neutralizing (K53Q) mutation, we observe proportionately lower phosphorylation extents due to the altered structural coupling, damped equilibrium fluctuations, and a more compact native ensemble. We thus establish a conformational selection mechanism for phosphorylation in the FF1 domain with K53 acting as a "gatekeeper", modulating the solvent exposure of the buried tyrosine. Our work demonstrates the role of unfavorable charge-charge interactions in governing functional events through the modulation of native ensemble characteristics, a feature that could be prevalent in ordered protein domains.

Global Dynamics Renders Protein Sites with High Functional Response

Deep mutational scanning enables examination of the effects of many mutations at each amino acid position in a query protein, readily disclosing positions that are particularly sensitive. Mutations in these positions alter protein function the most. Here, on the premise that dynamics underlie function, we explore to what extent the measured sensitivity to mutations could be linked to-perhaps be explained by-the structural dynamics of the protein. We employ a minimalist perturbation-response approach based on the Gaussian Network Model (GNM) on a data set of seven proteins with deep mutational scanning data. The analysis shows that the mutation-sensitive positions are often of capacity to modulate the global dynamics and to intermediate allosteric interactions in the structure. With that, upon strain perturbation, these positions decrease residue fluctuations the most, affecting function via entropy changes. This is particularly relevant for positions that are distant from binding sites or other functional regions of the protein and are sensitive to mutations, nevertheless. Our results indicate that mutations in these positions allosterically manipulate protein function.

Amide additives improve RDC measurements in polyacrylamide

Residual dipolar couplings (RDCs) provide valuable NMR parameters that can be used for structural calculation and verification. Measuring RDCs requires aligning macromolecules using one of various types of alignment media. Of different alignment media options, stretched or compressed polyacrylamide gels are advantageous due to their chemical stability. However, polyacrylamide interacts with proteins and significantly broadens NMR resonances. In this study, we found that the amide-containing compounds asparagine, glutamine and propionamide improve spectral quality of proteins in polyacrylamide gel without significantly reducing the magnitude of RDC values. Moreover, we showed that propionamide is an attractive additive that increases protein solubility without interfering with protein stability, ligand binding or NMR pulse width, suggesting its potential applications for our NMR methods.

Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis

Proteins in cellular environments are highly susceptible. Local perturbations to any residue can be sensed by other spatially distal residues in the protein molecule, showing long-range correlations in the native dynamics of proteins. The long-range correlations of proteins contribute to many biological processes such as allostery, catalysis, and transportation. Revealing the structural origin of such long-range correlations is of great significance in understanding the design principle of biologically functional proteins. In this work, based on a large set of globular proteins determined by X-ray crystallography, by conducting normal mode analysis with the elastic network models, we demonstrate that such long-range correlations are encoded in the native topology of the proteins. To understand how native topology defines the structure and the dynamics of the proteins, we conduct scaling analysis on the size dependence of the slowest vibration mode, average path length, and modularity. Our results quantitatively describe how native proteins balance between order and disorder, showing both dense packing and fractal topology. It is suggested that the balance between stability and flexibility acts as an evolutionary constraint for proteins at different sizes. Overall, our result not only gives a new perspective bridging the protein structure and its dynamics but also reveals a universal principle in the evolution of proteins at all different sizes.

The long-range correlated fluctuations are closely related to many biological processes of the proteins, such as catalysis, ligand binding, biomolecular recognition, and transportation. In this paper, we elucidate the structural origin of the long-range correlation and describe how native contact topology defines the slow-mode dynamics of the native proteins. Our result suggests an evolutionary constraint for proteins at different sizes, which may shed light on solving many biophysical problems such as structure prediction, multi-scale molecular simulations, and the design of molecular machines. Moreover, in statistical physics, as the long-range correlations are notable signs of the critical point, unveiling the origin of such criticality can extend our understanding of the organizing principle of a large variety of complex systems.

Allosteric control of metal-responsive transcriptional regulators in bacteria

Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.

Controlling Structure and Dimensions of a Disordered Protein via Mutations

The dimensions of intrinsically disordered proteins (IDPs) are sensitive to small energetic-entropic differences between intramolecular and protein–solvent interactions. This is commonly observed on modulating solvent composition and temperature. However, the inherently heterogeneous conformational landscape of IDPs is also expected to be influenced by mutations that can (de)stabilize pockets of local and even global structure, native and non-native, and hence the average dimensions. Here, we show experimental evidence for the remarkably tunable landscape of IDPs by employing the DNA-binding domain of CytR, a high-sequence-complexity IDP, as a model system. CytR exhibits a range of structure and compactness upon introducing specific mutations that modulate microscopic terms, including main-chain entropy, hydrophobicity, and electrostatics. The degree of secondary structure, as monitored by far-UV circular dichroism (CD), is strongly correlated to average ensemble dimensions for 14 different mutants of CytR and is consistent with the Uversky–Fink relation. Our experiments highlight how average ensemble dimensions can be controlled via mutations even in the disordered regime, the prevalence of non-native interactions and provide testable controls for molecular simulations.

Pressure accelerates the circadian clock of cyanobacteria

Although organisms are exposed to various pressure and temperature conditions, information remains limited on how pressure affects biological rhythms. This study investigated how hydrostatic pressure affects the circadian clock (KaiA, KaiB, and KaiC) of cyanobacteria. While the circadian rhythm is inherently robust to temperature change, KaiC phosphorylation cycles that were accelerated from 22 h at 1 bar to 14 h at 200 bars caused the circadian-period length to decline. This decline was caused by the pressure-induced enhancement of KaiC ATPase activity and allosteric effects. Because ATPase activity was elevated in the CI and CII domains of KaiC, while ATP hydrolysis had negative activation volumes (ΔV^≠), both domains played key roles in determining the period length of the KaiC phosphorylation cycle. The thermodynamic contraction of the structure of the active site during the transition state might have positioned catalytic residues and lytic water molecules favourably to facilitate ATP hydrolysis. Internal cavities might represent sources of compaction and structural rearrangement in the active site. Overall, the data indicate that pressure differences could alter the circadian rhythms of diverse organisms with evolved thermotolerance, as long as enzymatic reactions defining period length have a specific activation volume.

Slow Motion Protein Dance Visualized Using Red-Edge Excitation Shift of a Buried Fluorophore

It has been extremely challenging to detect protein structures with a dynamic core, such as dry molten globules, that remain in equilibrium with the tightly packed native (N) state and that are important for a myriad of entropy-driven protein functions. Here, we detect the higher entropy conformations of a human serum protein, using red-edge excitation shift experiments. We covalently introduced a fluorophore inside the protein core and observed that in a subset of native population, the side chains of the polar and buried residues have different spatial arrangements than the mean population and that they solvate the fluorophore on a timescale much slower than the nanosecond timescale of fluorescence. Our results provide direct evidence for the dense fluidity of protein core and show that alternate side-chain packing arrangements exist in the core that might be important for multiple binding functions of this protein.

Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition

Post-synaptic density-95, disks-large and zonula occludens-1 (PDZ) domains are small globular protein-protein interaction domains widely conserved from yeast to humans. They are composed of ∼90 amino acids and form a classical two α-helical/six β-strand structure. The prototypical ligand is the C-terminus of partner proteins; however, they also bind internal peptide sequences. Recent findings indicate that PDZ domains also bind phosphatidylinositides and cholesterol. Through their ligand interactions, PDZ domain proteins are critical for cellular trafficking and the surface retention of various ion channels. In addition, PDZ proteins are essential for neuronal signaling, memory, and learning. PDZ proteins also contribute to cytoskeletal dynamics by mediating interactions critical for maintaining cell-cell junctions, cell polarity, and cell migration. Given their important biological roles, it is not surprising that their dysfunction can lead to multiple disease states. As such, PDZ domain-containing proteins have emerged as potential targets for the development of small molecular inhibitors as therapeutic agents. Recent data suggest that the critical binding function of PDZ domains in cell signaling is more than just glue, and their binding function can be regulated by phosphorylation or allosterically by other binding partners. These studies also provide a wealth of structural and biophysical data that are beginning to reveal the physical features that endow this small modular domain with a central role in cell signaling.

Characterization of low-lying excited states of proteins by high-pressure NMR

Hydrostatic pressure alters the free energy of proteins by a few kJ mol^-1, with the amount depending on their partial molar volumes. Because the folded ground state of a protein contains cavities, it is always a state of large partial molar volume. Therefore pressure always destabilises the ground state and increases the population of partially and completely unfolded states. This is a mild and reversible conformational change, which allows the study of excited states under thermodynamic equilibrium conditions. Many of the excited states studied in this way are functionally relevant; they also seem to be very similar to kinetic folding intermediates, thus suggesting that evolution has made use of the 'natural' dynamic energy landscape of the protein fold and sculpted it to optimise function. This includes features such as ligand binding, structural change during the catalytic cycle, and dynamic allostery.

Seeking allosteric networks in PDZ domains

Ever since Ranganathan and coworkers subjected the covariation of amino acid residues in the postsynaptic density-95/Discs large/Zonula occludens 1 (PDZ) domain family to a statistical correlation analysis, PDZ domains have represented a paradigmatic family to explore single domain protein allostery. Nevertheless, several theoretical and experimental studies in the past two decades have contributed contradicting results with regard to structural localization of the allosteric networks, or even questioned their actual existence in PDZ domains. In this review, we first describe theoretical and experimental approaches that were used to probe the energetic network(s) in PDZ domains. We then compare the proposed networks for two well-studied PDZ domains namely the third PDZ domain from PSD-95 and the second PDZ domain from PTP-BL. Our analysis highlights the contradiction between the different methods and calls for additional work to better understand these allosteric phenomena.

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.

Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System

Allostery is a regulatory phenomenon whereby ligand binding to one site influences the binding of the same or a different ligand to another site on a macromolecule. The physical origins of allosteric regulation remain under intense investigation. In general terms, ligand-induced structural changes, perturbations of residue-specific dynamics, and surrounding solvent molecules all potentially contribute to the global energetics of allostery. While the role of solvent is generally well understood in regulatory events associated with major protein structural rearrangements, the degree to which protein dynamics impact solvent degrees of freedom is unclear, particularly in cases of dynamically driven allostery. With the aid of new crystal structures, extensive calorimetric and residue-specific dynamics studies over a range of time scales and temperatures, we dissect for the first time the relative degree to which changes in solvent entropy and residue-specific dynamics impact dynamically driven, allosteric inhibition of DNA binding by Zn in the zinc efflux repressor, CzrA (chromosomal zinc-regulated repressor). We show that non-native residue-specific dynamics in allosterically impaired CzrA mutants are accompanied by significant perturbations in solvent entropy that cannot be predicted from crystal structures. We conclude that functional dynamics are not necessarily restricted to protein residues but involve surface water molecules that may be responding to ligand (Zn)-mediated perturbations in protein internal motions that define the conformational ensemble, rather than major structural rearrangements.

Allosteric Self-Assembly of Coordinating Terthiophene Amphiphile for Triggered Light Harvesting

Allosteric regulation is extensively employed by nature to achieve functional control of protein or deoxyribonucleic acid through triggered conformational change at a remote site. We report that a similar strategy can be utilized in artificial self-assembly to control the self-assembled structure and its function. We show that on binding of metal ions to the headgroup of an amphiphile TTC4L, the conformational change may lead to change of the dipole orientation of the energy donor at the chain end. This on the one hand leads to a drastically different self-assembled structure; on the other hand, it enables light harvesting between the donor-acceptor. Because the Forster resonance fluorescence transfer efficiency is gated by metal ions, controlling the feeding of metal ions allows switching on and off of light harvesting. We expect that using allosteric self-assembly, we will be able to create abundant structures with distinct function from limited molecules, which show prominent potential for the postorganic modification of the structure and function of self-assembled materials.

Decomposing Dynamical Couplings in Mutated scFv Antibody Fragments into Stabilizing and Destabilizing Effects

Conformational fluctuations within scFv antibodies are characterized by a novel perturbation-response decomposition of molecular dynamics trajectories. Both perturbation and response profiles are stratified into stabilizing and destabilizing conditions. The linker between the VH and VL domains exhibits the dominant dynamical response by being coupled to nearly the entire protein, responding to both stabilizing and destabilizing perturbations. Perturbations within complementarity-determining regions (CDR) induce rich behavior in dynamic response. Among many effects, stabilizing any CDR loop in the VH domain triggers a destabilizing response in all CDR loops in the VL domain and vice versa. Destabilizing residues within the VL domain are likely to stabilize all CDR loops in the VH domain, and, when these residues are not buried, the CDR loops in the VL domain are also likely to be stabilized. These effects, described by shifts in normal mode characteristics, initiate a propensity for dynamic allostery with possible functional implications in bispecific antibodies.

A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations

Understanding the extent to which information is transmitted through the intramolecular interaction network of proteins upon a perturbation, that is, an allosteric effect, has long remained an unsolved problem. Through an analysis of high-resolution NMR data from the literature on 28 different proteins and 49 structural perturbations, we show that the extent of induced structural changes through mutations and molecular events including protein-protein, protein-peptide, protein-ligand binding, and post-translational modifications exhibit a near-universal exponential functional form. The extent of percolation into the protein structures can be up to 20-25 Å despite no apparent change in the 3D structures. These observations are also consistent with theoretical expectations, elementary graph theoretic analysis of protein structures, detailed molecular dynamics simulations, and experimental double-mutant cycles. Our analysis highlights that most molecular events would contribute to allosteric effects independent of protein structure, topology, or identity and provides a simple avenue to test and potentially model their effects.

Addressing the role of the α-helical extension in the folding of the third PDZ domain from PSD-95

PDZ domains are one of the most important protein-protein interaction domains in human. While presenting a conserved three dimensional structure, a substantial number of PDZ domains display structural extensions suggested to be involved in their folding and binding mechanisms. The C-terminal α-helix extension (α3) of the third PDZ domain from PSD-95 (PDZ3) has been reported to have a role in function of the domain as well as in the stabilization of the native fold. Here we report an evaluation of the effect of the truncation of this additional helix on the folding and unfolding kinetics of PDZ3. Fluorescent variants of full length and truncated PDZ3 were produced and stopped-flow fluorescence measurements were made under different experimental conditions (pH, ionic strength and temperature) to investigate the folding kinetics of the respective variant. The results show that folding of PDZ3 is robust and that the mechanism is only marginally affected by the truncation, which contributes to a destabilization of the native state, but otherwise do not change the overall observed kinetics. Furthermore, the increase in the unfolding rate constants, but not the folding rate constant upon deletion of α3 suggests that the α-helical extension is largely unstructured in the folding transition state.

New insight on the S100A1–STIP1 complex highlights the important relationship between allostery and entropy in protein function

Calcium signaling serves as a nexus of many vital cellular processes. Of particular importance is the role the calcium signaling plays in the prevention of protein misfolding, and the S100 family of calcium-binding proteins is a key player in this pathway. While the S100 proteins carry out a range of roles, the interaction of S100A1 and the stress-inducible phosphoprotein 1 (STIP1) has been shown to be particularly important. A recent study by Maciejewski et al. in Biochemical Journal (Biochemical Journal (2017) 474, 1853–1866) revealed new insights into the nature of the S100A1–STIP1 interaction. Not only did the present paper indicate the stoichiometry of binding for this interaction (three S100A1 dimers : one STIP1), it also demonstrated that the binding interaction is highly co-operative and that each S100A1–STIP1-binding interaction is entropically driven. The findings presented raise important new questions regarding the relationship between entropy and allostery in protein function. Recently, the dynamical underpinnings of allostery in protein function have become a topic of increased interest. A broad range of investigations have demonstrated that allostery can be mediated by entropic processes such as changes in the flexibility of the protein backbone and in the range of motions explored by side chains. The S100A1–STIP1 complex as described by Maciejewski et al. suggests a new system in which an allosteric-binding interaction driven by entropic processes may be systematically dissected in the future.

The Exact Nuclear Overhauser Enhancement: Recent Advances

Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of proteins. Here, we briefly revisit our most recent progress in the theory and use of exact nuclear Overhauser enhancements (eNOEs) for the calculation of structural ensembles that describe their conformational space. New developments are primarily targeted at increasing the number and improving the quality of extracted eNOE distance restraints, such that the multi-state structure calculation can be applied to proteins of higher molecular weights. We then review the implications of the exact NOE to the protein dynamics and function of cyclophilin A and the WW domain of Pin1, and finally discuss our current research and future directions.

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.

A dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein

An early intermediate during the base-induced unfolding of a multidomain protein resembles a dry molten globule state in which the structure is expanded without core hydration.

LK peptide side chain dynamics at interfaces are independent of secondary structure

Real-time observation of the ultrafast motions of leucine side chains within model peptides at the water–air interface with representative folds – α-helix, 3₁₀-helix, β-strand – show that interfacial dynamics are mostly determined by surface interactions.