Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting

The evolving role of hydrogen/deuterium exchange mass spectrometry in early-stage drug discovery

Protein function relies on protein dynamics and therefore dynamical information can be crucial for drug discovery of challenging protein targets. Assessing protein dynamics experimentally has traditionally been nontrivial. However, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) is now an established technique that can expose details about changes in protein dynamics, binding sites and allostery at the peptide level. HDX-MS is a versatile and powerful biophysical tool to gain insights into the workings of numerous protein systems and complexes. Advances in instrumentation, automation, data analysis, and interpretation over the past two decades have led to increased uptake and democratization of HDX-MS in both academic and industry settings. Here, we outline the current uses of HDX-MS in early-stage drug discovery and illustrate the interplay with computational chemistry to maximize the value of data obtained from HDX-MS experiments. Finally, we consider approaches which may aid structural interpretation of HDX-MS data in the coming years.

The Pseudomonas aeruginosa PhuS proximal ligand His-209 triggers a conformational switch in function from DNA binding to heme transfer

Pseudomonas aeruginosa can acquire iron from heme via the heme assimilation system and Pseudomonas heme uptake (Phu) systems. Heme uptake is regulated at the metabolic level by the cytoplasmic protein PhuS that controls heme flux through a heme oxygenase HemO, releasing iron and biliverdin IXβ and IXδ. We have shown PhuS regulates extracellular heme flux, and in its apo-form transcriptionally regulates the iron and heme-dependent small RNAs (sRNAs) PrrF/PrrH. This mutual exclusivity of function is driven by conformational rearrangement of PhuS on heme binding. Herein, we show through a combination of EMSA and fluorescence anisotropy that mutation of the His-209 proximal ligand allows both apo- and holo-PhuS H209A to bind to the prrF1 promoter with significantly lower affinity when compared to PAO1 WT. Hydrogen deuterium exchange coupled to mass spectrometry revealed the apo- and holo-PhuS H209A structures are closer to each other than their WT counterparts and sample a conformational landscape between the apo- and holo-PhuS WT conformations, that is neither optimal for heme transfer nor DNA-binding. Furthermore, quantitative PCR and Western blot analysis of the phuSH209A allelic strain compared to PAO1 WT revealed an uncoupling of the PhuS-HemO dependent regulation of heme flux into the cell that abrogates the heme dependent regulation of the PrrF/PrrH sRNAs. The data supports a model where heme coordination through His-209 drives the conformational switch that determines mutual exclusivity in function of apo- and holo-PhuS. This dual function of PhuS is central to integrating extracellular heme utilization into the PrrF/PrrH sRNA regulatory network critical for P. aeruginosa adaptation within the host.

Structural dynamics of the dengue virus non-structural 5 (NS5) interactions with promoter stem-loop A (SLA)

The dengue virus (DENV) NS5 protein, essential for viral RNA synthesis, is an attractive antiviral drug target. DENV NS5 interacts with the stem-loop A (SLA) promoter at the 5'-untranslated region of the viral genome to initiate negative-strand synthesis. However, the conformational dynamics of this interaction remains unclear. Our study explores the structural dynamics of DENV serotype 2 NS5 (DENV2 NS5) in complex with SLA, employing surface plasmon resonance (SPR), hydrogen-deuterium exchange mass spectrometry (HDX-MS), computational modeling, and cryoEM. Our findings reveal that DENV2 NS5 binds SLA in a closed conformation, with interdomain cooperation between its methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, critical for the interaction. SLA binding induces conformational changes in both domains, highlighting NS5's multifunctional role in viral replication. Our cryoEM results visualizes the DENV2 NS5-SLA complex, confirming a conserved SLA binding across DENV serotypes and provides key insights for antiviral strategies targeting NS5's conformational states.

Mapping the distribution and affinities of ligand interaction sites on human serum albumin

Ligands in many instances interact with a protein at multiple sites with a range of affinities. In this study, ligand-protein interaction sites on human serum albumin (HSA) are mapped using the site-identification by ligand competitive saturation (SILCS)-Biologics approach in conjunction with hydrogen-deuterium exchange (HDX)-mass spectrometry (MS) experiments. Ligands studied include known HSA binders, ibuprofen and ketoprofen, and compounds arginine, alanine, sucrose, and trehalose, excipients used in therapeutic formulations of protein-based drugs. In addition, the impact of excipient binding to HSA on its stability is investigated through temperature-ramp stability studies monitoring solution viscosity. For the studied ligands, interactions that correspond to known drug-binding sites (DSs) are identified. These include previously identified ibuprofen and ketoprofen interaction sites as well as additional sites and, in the case of the excipients, the ligands are shown to also bind at previously unidentified interaction sites, termed excipient sites (ESs) with 20 or more sites identified for the studied compounds. HDX-MS titrations were used to determine dissociation constants for a subset of the interaction sites for ibuprofen, ketoprofen, arginine, and sucrose, which exhibited Kd values in the low micromolar to millimolar range in satisfactory agreement with SILCS-Biologics predicted affinities, validating the computational approach to identify both high- and low-affinity interaction sites. The stability studies indicate the excipients offer protection at low excipient/protein ratios up to 66 with destabilization occurring at ratios above 132 with the exception of sucrose at the t0 time point, indicating that the more favorable affinities of sucrose seen in the SILCS-Biologics and HDX-MS analyses contribute to protein stabilization. These results indicate that ligands can bind to large numbers of interaction sites on proteins, with those interactions having implications for the development of formulations for therapeutic proteins.

Structure Characterization of a Disordered Peptide Using In-Droplet Hydrogen/Deuterium Exchange Mass Spectrometry and Molecular Dynamics

In-droplet hydrogen/deuterium exchange (HDX)-mass spectrometry (MS) experiments have been conducted for peptides of highly varied conformational type. A new model is presented that combines the use of protection factors (PF) from molecular dynamics (MD) simulations with intrinsic HDX rates (k int) to obtain a structure-to-reactivity calibration curve. Using the model, the relationship of peptide structural flexibility and HDX reactivity for different peptides is elucidated. Additionally, the model is used to describe the degree of conformational flexibility and structural bias for the disease-relevant Nt17 peptide; although highly flexible, intrinsically primed for facile conversion to α-helical conformation upon binding with molecular partners imparts significant in-droplet HDX protection for this peptide. In the future, a scale may be developed whereby HDX reactivity is predictive of the degree of structural flexibility and bias (propensity to form 2° structural elements such as α-helix, β-sheet, and β-turn) for intrinsically disordered regions (IDRs). Such structural resolution may ultimately be used for high-throughput screening of IDR structural transformation(s) upon binding of ligands such as drug candidates.

Structural Dynamics of the Dengue Virus Non-structural 5 (NS5) Interactions with Promoter Stem Loop A (SLA)

The dengue virus (DENV) NS5 protein plays a central role in dengue viral RNA synthesis which makes it an attractive target for antiviral drug development. DENV NS5 is known to interact with the stem-loop A (SLA) promoter at the 5'-untranslated region (5'-UTR) of the viral genome as a molecular recognition signature for the initiation of negative strand synthesis at the 3' end of the viral genome. However, the conformational dynamics involved in these interactions are yet to be fully elucidated. Our study explores the structural dynamics of NS5 from DENV serotype 2 (DENV2 NS5) in complex with SLA, employing surface plasmon resonance (SPR), hydrogen - deuterium exchange coupled to mass spectrometry (HDX-MS), computational modeling, and cryoEM single particle analysis to delineate the molecular details of their interaction. Our findings indicate that DENV2 NS5 binds SLA in a closed conformation with significant interdomain cooperation between the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, a feature integral to the interaction. Our HDX-MS studies reveal SLA-induced conformational changes in both domains of DENV2 NS5, reflecting a potential mechanism for dengue NS5's multifunctional role in viral replication. Lastly, our cryoEM structure provides the first visualization of the DENV2 NS5-SLA complex, confirming a conserved SLA binding mode across DENV serotypes. These insights obtained from our study enhance our understanding of dengue NS5's complex conformational landscape, supporting the potential development of antiviral strategies targeting dengue NS5's conformational states.

Integration of Hydrogen-Deuterium Exchange Mass Spectrometry with Molecular Dynamics Simulations and Ensemble Reweighting Enables High Resolution Protein-Ligand Modeling

Hydrogen-Deuterium exchange mass spectrometry's (HDX-MS) utility in identifying and characterizing protein-small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein-ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen-Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein-small molecule ligand interactions. To that end, we employ a strategy combining computational protein-ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein-ligand pairs tested, the HDX derived protein-ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.

Hydrogen/Deuterium Exchange Mass Spectrometry: Fundamentals, Limitations, and Opportunities

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) probes dynamic motions of proteins by monitoring the kinetics of backbone amide deuteration. Dynamic regions exhibit rapid HDX, while rigid segments are more protected. Current data readouts focus on qualitative comparative observations (such as "residues X to Y become more protected after protein exposure to ligand Z"). At present, it is not possible to decode HDX protection patterns in an atomistic fashion. In other words, the exact range of protein motions under a given set of conditions cannot be uncovered, leaving space for speculative interpretations. Amide back exchange is an under-appreciated problem, as the widely used (m-m0)/(m100-m0) correction method can distort HDX kinetic profiles. Future data analysis strategies require a better fundamental understanding of HDX events, going beyond the classical Linderstrøm-Lang model. Combined with experiments that offer enhanced spatial resolution and suppressed back exchange, it should become possible to uncover the exact range of motions exhibited by a protein under a given set of conditions. Such advances would provide a greatly improved understanding of protein behavior in health and disease.

Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry

This paper sheds light on the meaning of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) data. HDX-MS data provide not structural information but dynamic information on an analyte protein. First, the reaction mechanism of backbone amide HDX reaction is considered and the correlation between the parameters from an X-ray crystal structure and the protection factors of HDX reactions of cytochrome c is evaluated. The presence of H-bonds in a protein structure has a strong influence on HDX rates which represent protein dynamics, while the solvent accessibility only weakly affects the HDX rates. Second, the energy diagrams of the HDX reaction at each residue in the presence and absence of perturbation are described. Whereas the free energy change upon mutation can be directly measured by the HDX rates, the free energy change upon ligand binding may be complicated due to the presence of unbound analyte protein in the protein-ligand mixture. Third, the meanings of HDX and other biophysical techniques are explained using a hypothetical protein folding well. The shape of the protein folding well describes the protein dynamics and provides Boltzmann distribution of open and closed states which yield HDX protection factors, while a protein's crystal structure represents a snapshot near the bottom of the well. All biophysical data should be consistent yet provide different information because they monitor different parts of the same protein folding well.

The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control

Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.

Integrating Hydrogen Deuterium Exchange-Mass Spectrometry with Molecular Simulations Enables Quantification of the Conformational Populations of the Sugar Transporter XylE

A yet unresolved challenge in structural biology is to quantify the conformational states of proteins underpinning function. This challenge is particularly acute for membrane proteins owing to the difficulties in stabilizing them for in vitro studies. To address this challenge, we present an integrative strategy that combines hydrogen deuterium exchange-mass spectrometry (HDX-MS) with ensemble modeling. We benchmark our strategy on wild-type and mutant conformers of XylE, a prototypical member of the ubiquitous Major Facilitator Superfamily (MFS) of transporters. Next, we apply our strategy to quantify conformational ensembles of XylE embedded in different lipid environments. Further application of our integrative strategy to substrate-bound and inhibitor-bound ensembles allowed us to unravel protein-ligand interactions contributing to the alternating access mechanism of secondary transport in atomistic detail. Overall, our study highlights the potential of integrative HDX-MS modeling to capture, accurately quantify, and subsequently visualize co-populated states of membrane proteins in association with mutations and diverse substrates and inhibitors.

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.

Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data

Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about the structural determinants of hydrogen exchange itself, such data have successfully helped guide the structural modeling of challenging molecular systems, such as membrane proteins or large macromolecular complexes. As hydrogen-exchange monitoring provides information on the dynamics of molecules in solution, it can complement other experimental techniques in so-called integrative modeling approaches. However, hydrogen-exchange data have often only been used to qualitatively assess molecular structures produced by computational modeling tools. In this paper, we look beyond qualitative approaches and survey the various paradigms under which hydrogen-exchange data have been used to quantitatively guide the computational modeling of molecular structures. Although numerous prediction models have been proposed to link molecular structure and hydrogen exchange, none of them has been widely accepted by the structural biology community. Here, we present as many hydrogen-exchange prediction models as we could find in the literature, with the aim of providing the first exhaustive list of its kind. From purely structure-based models to so-called fractional-population models or knowledge-based models, the field is quite vast. We aspire for this paper to become a resource for practitioners to gain a broader perspective on the field and guide research toward the definition of better prediction models. This will eventually improve synergies between hydrogen-exchange monitoring and molecular modeling.

Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]

Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.