Protein conformational switches: from nature to design

Molecular Modelling in Bioactive Peptide Discovery and Characterisation

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties and interactions with biological targets. Many models predicting bioactive peptide function or structure rely on their intrinsic properties, including the influence of amino acid composition, sequence, and chain length, which impact stability, folding, aggregation, and target interaction. Homology modelling predicts peptide structures based on known templates. Peptide-protein interactions can be explored using molecular docking techniques, but there are challenges related to the inherent flexibility of peptides, which can be addressed by more computationally intensive approaches that consider their movement over time, called molecular dynamics (MD). Virtual screening of many peptides, usually against a single target, enables rapid identification of potential bioactive peptides from large libraries, typically using docking approaches. The integration of artificial intelligence (AI) has transformed peptide discovery by leveraging large amounts of data. AlphaFold is a general protein structure prediction tool based on deep learning that has greatly improved the predictions of peptide conformations and interactions, in addition to providing estimates of model accuracy at each residue which greatly guide interpretation. Peptide function and structure prediction are being further enhanced using Protein Language Models (PLMs), which are large deep-learning-derived statistical models that learn computer representations useful to identify fundamental patterns of proteins. Recent methodological developments are discussed in the context of canonical peptides, as well as those with modifications and cyclisations. In designing potential peptide therapeutics, the main outstanding challenge for these methods is the incorporation of diverse non-canonical amino acids and cyclisations.

Conformational switches in human RNA binding proteins involved in neurodegeneration

Conformational switching in RNA binding proteins (RBPs) is crucial for regulation of RNA processing and transport. Dysregulation or mutations in RBPs and broad RNA processing abnormalities are related to many human diseases including neurodegenerative disorders. Here, we review the role of protein-RNA conformational switches in RBP-RNA complexes. RBP-RNA complexes exhibit wide range of conformational switching depending on the RNA molecule and its ability to induce conformational changes in its partner RBP. We categorize the conformational switches into three groups: rigid body, semi-flexible and full flexible. We also investigate conformational switches in large cellular assemblies including ribosome, spliceosome and RISC complexes. In addition, the role of intrinsic disorder in RBP-RNA conformational switches is discussed. We have also discussed the effect of different disease-causing mutations on conformational switching of proteins associated with neurodegenerative diseases. We believe that this study will enhance our understanding on the role of protein-RNA conformational switches. Furthermore, the availability of a large number of atomic structures of RBP-RNA complexes in near future would facilitate to create a complete repertoire of human RBP-RNA conformational switches.

Uncovering layer by layer the risk of nanoplastics to the environment and human health

Nanoplastics (NPs), defined as plastic particles with dimensions less than 100 nm, have emerged as a persistent environmental contaminant with potential risk to both environment and human health. Nanoplastics might translocate across biological barriers and accumulate in vital organs, leading to inflammatory responses, oxidative stress, and genotoxicity, already reported in several organisms. Disruptions to cellular functions, hormonal balance, and immune responses were also linked to NPs exposure in in vitro assays. Further, NPs have been found to adsorb other pollutants, such as persistent organic pollutants (POPs), and leach additives potentially amplifying their advere impacts, increasing the threat to organisms greater than NPs alone. However, NPs toxic effects remain largely unexplored, requiring further research to elucidate potential risks to human health, especially their accumulation, degradation, migration, interactions with the biological systems and long-term consequences of chronic exposure to these compounds. This review provides an overview of the current state-of-art regarding NPs interactions with environmental pollutants and with biological mechanisms and toxicity within cells.

Aromatic-aromatic interactions drive fold switch of GA95 and GB95 with three residue difference

Proteins typically adopt a single fold to carry out their function, but metamorphic proteins, with multiple folding states, defy this norm. Deciphering the mechanism of conformational interconversion of metamorphic proteins is challenging. Herein, we employed nuclear magnetic resonance (NMR), circular dichroism (CD), and all-atom molecular dynamics (MD) simulations to elucidate the mechanism of fold switching in proteins GA95 and GB95, which share 95% sequence homology. The results reveal that long-range interactions, especially aromatic π-π interactions involving residues F52, Y45, F30, and Y29, are critical for the protein switching from a 3α to a 4β + α fold. This study contributes to understanding how proteins with highly similar sequences fold into distinct conformations and may provide valuable insights into the protein folding code.

Terminal Tryptophan-Directed Anisotropic Self-Assembly for Precise Protein Nanostructure Regulation

A common challenge in nanotechnology is synthesizing nanomaterials with well-defined structures. In particular, it remains a major unresolved challenge to precisely regulate the structure and function of protein nanomaterials, which are structurally diverse, highly ordered, and complex and offer an innovative means that enables a high performance in various nanodevices, which is rarely achievable with other nanomaterials. Here an innovative approach is proposed to fabricating multi-dimensional (0- to 3D) protein nanostructures with functional and structural specialties via molecular-level regulation. This approach is based on a stable, consistent, anisotropic self-assembly of Tobacco mosaic virus (TMV) coat protein-derived engineered building blocks where genetically added tryptophan residues are externally tailored. The unique structural characteristics of each nanostructure above are demonstrated in detail through various analyses (electron microscopy, atomic force microscopy, dynamic light scattering, and small-angle X-ray scattering) and further investigated through molecular dynamics simulations, indicating that this control, anisotropic, and molecular assembly-based approach to regulating protein nanostructures holds great potential for customizing a variety of nanomaterials with unique functions and structures.

The interaction networks of small rubber particle proteins in the latex of Taraxacum koksaghyz reveal diverse functions in stress responses and secondary metabolism

The Russian dandelion (Taraxacum koksaghyz) is a promising source of natural rubber (NR). The synthesis of NR takes place on the surface of organelles known as rubber particles, which are found in latex - the cytoplasm of specialized cells known as laticifers. As well as the enzymes directly responsible for NR synthesis, the rubber particles also contain small rubber particle proteins (SRPPs), the most abundant of which are SRPP3, 4 and 5. These three proteins support NR synthesis by maintaining rubber particle stability. We used homology-based searches to identify the whole TkSRPP gene family and qPCR to create their spatial expression profiles. Affinity enrichment-mass spectrometry was applied to identify TkSRPP3/4/5 protein interaction partners in T. koksaghyz latex and selected interaction partners were analyzed using qPCR, confocal laser scanning microscopy and heterologous expression in yeast. We identified 17 SRPP-like sequences in the T. koksaghyz genome, including three apparent pseudogenes, 10 paralogs arranged as an inverted repeat in a cluster with TkSRPP3/4/5, and one separate gene (TkSRPP6). Their sequence diversity and different expression profiles indicated distinct functions and the latex interactomes obtained for TkSRPP3/4/5 suggested that TkSRPP4 is a promiscuous hub protein that binds many partners from different compartments, whereas TkSRPP3 and 5 have more focused interactomes. Two interactors shared by TkSRPP3/4/5 (TkSRPP6 and TkUGT80B1) were chosen for independent validation and detailed characterization. TkUGT80B1 triterpenoid glycosylating activity provided first evidence for triterpenoid saponin synthesis in T. koksaghyz latex. Based on its identified interaction partners, TkSRPP4 appears to play a special role in the endoplasmic reticulum, interacting with lipidmodifying enzymes that may facilitate rubber particle formation. TkSRPP5 appears to be involved in GTPase-dependent signaling and TkSRPP3 may act as part of a kinase signaling cascade, with roles in stress tolerance. TkSRPP interaction with TkUGT80B1 draws a new connection between TkSRPPs and triterpenoid saponin synthesis in T. koksaghyz latex. Our data contribute to the functional differentiation between TkSRPP paralogs and demonstrate unexpected interactions that will help to further elucidate the network of proteins linking TkSRPPs, stress responses and NR biosynthesis within the cellular complexity of latex.

Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy

Inspired by the success of deep learning in predicting static protein structures, researchers are now actively exploring other deep learning algorithms aimed at predicting the conformational changes of proteins. Currently, a major challenge in the development of such models lies in the limited training data characterizing different conformational transitions. To address this issue, molecular dynamics simulations is combined with enhanced sampling methods to create a large-scale database. To this end, the study simulates the conformational changes of 2635 proteins featuring two known stable states, and collects the structural information along each transition pathway. Utilizing this database, a general deep learning model capable of predicting the transition pathway for a given protein is developed. The model exhibits general robustness across proteins with varying sequence lengths (ranging from 44 to 704 amino acids) and accommodates different types of conformational changes. Great agreement is shown between predictions and experimental data in several systems and successfully apply this model to identify a novel allosteric regulation in an important biological system, the human β-cardiac myosin. These results demonstrate the effectiveness of the model in revealing the nature of protein conformational changes.

Conformational Switch of a Peptide Provides a Novel Strategy to Design Peptide Loaded Porous Organic Polymer for Pyroptosis Pathway Mediated Cancer Therapy

While peptide-based drug development is extensively explored, this strategy has limitations due to rapid excretion from the body (or shorter half-life in the body) and vulnerability to protease-mediated degradation. To overcome these limitations, a novel strategy for the development of a peptide-based anticancer agent is introduced, utilizing the conformation switch property of a chameleon sequence stretch (PEP1) derived from a mycobacterium secretory protein, MPT63. The selected peptide is then loaded into a new porous organic polymer (PG-DFC-POP) synthesized using phloroglucinol and a cresol derivative via a condensation reaction to deliver the peptide selectively to cancer cells. Utilizing ensemble and single-molecule approaches, this peptide undergoes a transition from a disordered to an alpha-helical conformation, triggered by the acidic environment within cancer cells that is demonstrated. This adopted alpha-helical conformation resulted in the formation of proteolysis-resistant oligomers, which showed efficient membrane pore-forming activity selectively for negatively charged phospholipids accumulated in cancer cell membranes. The experimental results demonstrated that the peptide-loaded PG-DFC-POP-PEP1 exhibited significant cytotoxicity in cancer cells, leading to cell death through the Pyroptosis pathway, which is established by monitoring numerous associated events starting from lysosome membrane damage to GSDMD-induced cell membrane demolition. This novel conformational switch-based drug design strategy is believed to have great potential in endogenous environment-responsive cancer therapy and the development of future drug candidates to mitigate cancers.

Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations

Cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.

Structure prediction of alternative protein conformations

Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB. However, almost all protein structures with multiple conformations represented in the PDB have been used while training these models. Therefore, it is unclear whether alternative protein conformations can be genuinely predicted using these networks, or if they are simply reproduced from memory. Here, we train a structure prediction network, Cfold, on a conformational split of the PDB to generate alternative conformations. Cfold enables efficient exploration of the conformational landscape of monomeric protein structures. Over 50% of experimentally known nonredundant alternative protein conformations evaluated here are predicted with high accuracy (TM-score > 0.8).

Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein

Hydrogen-bonding (H-bonding) interactions in metalloprotein active sites can critically regulate enzyme function. Changes in the protein structure triggered by interplay with substrates, products, and partner proteins are often translated to the metallocofactor by way of specific changes in H-bond networks connected to the active site. However, the complexities of metalloprotein architecture and mechanism often preclude our ability to define the precise molecular interactions giving rise to these intricate regulatory pathways. To address this shortcoming, we have developed conformationally switchable artificial metalloproteins (swArMs) in which allosteric Gln-binding triggers protein conformational changes that impact the microenvironment surrounding an installed metallocofactor. Herein, we report a combined structural, spectroscopic, and computational approach to enhance the conformation-dependent changes in H-bond interactions surrounding the metallocofactor site of a swArM. Structure-informed molecular dynamics simulations were employed to predict point mutations that could enhance active site H-bond interactions preferentially in the Gln-bound holo-conformation of the swArM. Testing our predictions via the unique infrared spectral signals associated with the metallocofactor site, we have identified three key residues capable of imparting conformational control over the metallocofactor microenvironment. The resultant swArMs not only model biologically relevant structural regulation but also provide an enhanced Gln-responsive biological probe to be leveraged in future biosensing applications.

Unnatural enzyme activation by a metal-responsive regulatory protein

As a result of calcium ion binding, the calcium-dependent regulatory protein calmodulin (CaM) undergoes a conformational change, enabling it to bind to and activate a variety of enzymes. However, the detoxification enzyme glutathione S-transferase (GST) is notably not among the enzymes activated by CaM. In this study, we demonstrate the feasibility of establishing, in vitro, an artificial regulatory link between CaM and GST using bifunctional chemical transducer (CT) molecules possessing binders for CaM and GST. We show that the CTs convert the constitutively active GST into a triggerable enzyme whose activity is unnaturally regulated by the CaM conformational state and consequently, by the level of calcium ions. The ability to reconfigure the regulatory function of CaM demonstrates a novel mode by which CTs could be employed to mediate artificial protein crosstalk, as well as a new means to achieve artificial control of enzyme activity by modulating the coordination of metal ions. Within this study, we also investigated the impact of covalent interaction between the CTs and the enzyme target. This investigation offers further insights into the mechanisms governing the function of CTs and the possibility of rendering them isoform specific.

Immune targeting of filarial glutaredoxin through a multi-epitope peptide-based vaccine: A reverse vaccinology approach

Despite the efforts of global programme to eliminate lymphatic filariasis (GPELF), the threat of lymphatic filariasis (LF) still looms over humanity in terms of long-term disabilities, and morbidities across the globe. In light of this situation, investigators have chosen to focus on the development of immunotherapeutics targeting the physiologically important filarial-specific proteins. Glutaredoxin (16.43 kDa) plays a pivotal role in filarial redox biology, serving as a vital contributor. In the context of the intra-host survival of filarial parasites, this antioxidant helps in mitigating the oxidative stress imposed by the host immune system. Given its significant contribution, the development of a vaccine targeting glutaredoxin holds promise as a new avenue for achieving a filaria-free world. Herein, multi-epitope-based vaccine was designed using advanced immunoinformatics approach. Initially, 4B-cell epitopes and 6 T-cell epitopes (4 MHC I and 2 MHC II) were identified from the 146 amino acid long sequence of glutaredoxin of the human filarid, Wuchereria bancrofti. Subsequent clustering of these epitopes with linker peptides finalized the vaccine structure. To boost TLR-mediated innate immunity, TLR-specific adjuvants were incorporated into the designed vaccine. After that, experimental analyses confirm the designed vaccine, Vac4 as anefficient ligand of human TLR5 to elicit protective innate immunity against filarial glutaredoxin. Immune simulation further demonstrated abundant levels of IgG and IgM as crucial contributors in triggering vaccine-induced adaptive responses in the recipients. Hence, to facilitate the validation of immunogenicity of the designed vaccine, Vac4 was cloned in silico in pET28a(+) expression vector for recombinant production. Taken together, our findings suggest that vaccine-mediated targeting of filarial glutaredoxin could be a future option for intervening LF on a global scale.

Circular Heterochiral Titanium-Based Self-Assembled Architectures

Circular trinuclear helicates have been synthesized from a bis-biphenol strand (LH4), titanium isopropoxide, and various diimine ligands. These self-assembled architectures constructed around three TiO4N2 nodes have a heterochiral structure (C1 symmetry) when 2,2'-bipyridine (A), 4,4'-dimethyl-2,2'-bipyridine (B), 4,4'-bromo-2,2'-bipyridine (C), or 4,4'-dimethyl-2,2'-bipyrimidine (D) is employed. Within these complexes, one nitrogen ligand is endo-positioned inside the metallo-macrocycle, whereas the other two diimine ligands point outside the helicate framework. This investigation highlights that the nitrogen ligand which does not participate in the helicate framework of the complex controls the overall symmetry of the helicate since the 2,2'-bipyrimidine chelate (F) ends in the formation of a homochiral aggregate (C3 symmetry). The lack of symmetry found in the solid state for the trinuclear species ([Ti3L3(B)3], [Ti3L3(C)3], and [Ti3L3(D)3]) is observed for these complexes in solution (dichloromethane or chloroform). Remarkably, the 2,2'-bipyrazine ligand (ligand E) ends in the formation of a hexameric aggregate formulated as [Ti6L6(E)6], whereas the use of 4,4'-dimethyl-2,2'-bipyrimidine (ligand D) permits to generate the dinuclear complexes ([Ti2L(D)2(OiPr)4] and [Ti2L2(D)2]) in addition to the trimeric structure [Ti3L3(D)3]. The behavior of [Ti3L3(A)3] in solution, on the other hand, is unique since an equilibrium between the homochiral and the heterochiral form is reached within 17 days after the complex has been dissolved in dichloromethane (C3-[Ti3L3(A)3]/C1-[Ti3L3(A)3] ratio = 0.3). In chloroform, the heterochiral form of [Ti3L3(A)3] is stable for the same period of time, evidencing the dependence of this stereochemical transformation toward the solvent medium. The thermodynamic and kinetic parameters linked to this stereochemical equilibrium have been obtained and point to the fact that the transformation is intramolecular and not induced by the presence of external ligands. The thermodynamic constant of the C1-[Ti3L3(A)3]/C3-[Ti3L3(A)3] equilibrium is found to be K = 0.34 ± 10%. Further evidence to rationalize this solvent-induced symmetry switch is obtained via a DFT calculation and classical molecular dynamics. In particular, this computational investigation elucidates the reason why the stereochemical transformation of a heterochiral architecture into a homochiral structure is possible only for a trinuclear assembly containing ligand A.

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1  . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.

Macrocyclic Conformational Switch Coupled with Pyridinium-Induced PET for Fluorescence Detection of Adenosine Triphosphate

The binding of nucleotides is crucial for signal transduction as it induces conformational protein changes, leading to downstream cellular responses. Synthetic receptors that bind nucleotides and transduce the binding event into global conformational rearrangements are highly challenging to design, especially those that operate in an aqueous solution. Much work is focused on evaluating functionalized dyes to detect nucleotides, whereas coupling of a nucleotide-induced conformational switching to a sensing event has not been reported to date. We disclose synthetic receptors that undergo a global conformational rearrangement upon nucleotide binding. Integrating naphthalimide and the pyridinium ion into the structure enables stabilization of the folded conformation and efficient fluorescence quenching. The binding of a nucleotide rearranges the receptor conformation and alters the strong fluorescence enhancement. The methylpyridinium-containing receptor demonstrated high sensing selectivity for adenosine 5'-triphosphate (ATP) and a record 160-fold fluorescence enhancement. It can detect fluctuations of ATP in HeLa cells and possesses low cytotoxicity. The developed systems present an attractive approach for designing ATP-responsive artificial molecular switches that operate in water and integrate a strong fluorescence response.

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.

Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry

We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection using XL-MS data. For conformer selection, we developed two scores-the monolink probability score (MP) and the crosslink probability score (XLP)-both of which are based on residue depth from the protein surface. We benchmarked MP and XLP on a large dataset of decoy protein structures and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein, first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles-or a conformation within 1 Å of this model-was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of glutamine-binding periplasmic protein, and these results were further improved by including the "occupancy" of the monolinks. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models. The MP and XLP scoring functions mentioned above are available at https://gitlab.com/topf-lab/xlms-tools.

Designed allosteric protein logic

The regulation of protein function by external or internal signals is one of the key features of living organisms. The ability to directly control the function of a selected protein would represent a valuable tool for regulating biological processes. Here, we present a generally applicable regulation of proteins called INSRTR, based on inserting a peptide into a loop of a target protein that retains its function. We demonstrate the versatility and robustness of coiled-coil-mediated regulation, which enables designs for either inactivation or activation of selected protein functions, and implementation of two-input logic functions with rapid response in mammalian cells. The selection of insertion positions in tested proteins was facilitated by using a predictive machine learning model. We showcase the robustness of the INSRTR strategy on proteins with diverse folds and biological functions, including enzymes, signaling mediators, DNA binders, transcriptional regulators, reporters, and antibody domains implemented as chimeric antigen receptors in T cells. Our findings highlight the potential of INSRTR as a powerful tool for precise control of protein function, advancing our understanding of biological processes and developing biotechnological and therapeutic interventions.

Reversible conformational switching of a photo-responsive ortho-azobenzene/2,6-pyridyldicarboxamide heterofoldamer

We report on a convenient synthetic route to rapidly access a new photo-responsive ortho-azobenzene/2,6-pyridyldicarboxamide heterofoldamer. The adoption of a stable helical conformation has been established for this scaffold in both the solid state and in solution using single crystal X-ray diffraction and circular dichroism (CD) spectroscopy respectively. Reversible control over the stimuli-driven structural re-ordering of the supramolecular scaffold, from a stable helical conformation under non-irradiative conditions, to a less well-ordered state under irradiative conditions, has been identified. The robust nature of the responsive, conformational, molecular switching behaviour has been determined using UV/Vis, 1H NMR and CD spectroscopy. Minimal loss in the efficiency of the stimuli-driven, structural re-ordering processes of the foldamer scaffold is observed, even upon multiple cyclic treatments with irradiative/non-irradiative conditions.

Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers

To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.

Design of stimulus-responsive two-state hinge proteins

In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of "hinge" proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.

Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon

Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments-such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host proteins, such as ACE2 receptor. Machaon's meta-analysis of the results highlights structural, chemical and transcriptional similarities between the Spike monomer and human proteins, indicating a multi-level viral mimicry. This extended analysis also revealed relationships of the Spike protein with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://machaonweb.com .

Strategies for Conditional Regulation of Proteins

Design of the next-generation of therapeutics, biosensors, and molecular tools for basic research requires that we bring protein activity under control. Each protein has unique properties, and therefore, it is critical to tailor the current techniques to develop new regulatory methods and regulate new proteins of interest (POIs). This perspective gives an overview of the widely used stimuli and synthetic and natural methods for conditional regulation of proteins.

pH-Triggered Recovery of Organic Polymer Photocatalytic Particles for the Production of High Value Compounds and Enhanced Recyclability

Pseudo-homogeneous polymeric photocatalysts are an emerging class of highly efficient and tunable photocatalytic materials, where the photocatalytic centers are easily accessible. The creation of highly efficient photocatalytic materials that can be rapidly separated and recovered is one of the critical challenges in photocatalytic chemistry. Here, we describe pH-responsive photocatalytic nanoparticles that are active and well-dispersed under acidic conditions but aggregate instantly upon elevation of pH, enabling easy recovery. These responsive photocatalytic polymers can be used in various photocatalytic transformations, including Cr^VI reduction and photoredox alkylation of indole derivative. Notably, the cationic nature of the photocatalyst accelerates reaction rate of an anionic substrate compared to uncharged species. These photocatalytic particles could be readily recycled allowing multiple successive photocatalytic reactions with no clear loss in activity.

Design and characterization of a protein fold switching network

To better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β-grasp, and α/β-plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β-grasp fold in the smaller form but an α/β-plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery

The NtrC family of proteins senses external stimuli and accordingly stimulates stress and virulence pathways via activation of associated σ⁵⁴-dependent RNA polymerases. However, the structural determinants that mediate this activation are not well understood. Here, we establish using computational, structural, biochemical, and biophysical studies that MopR, an NtrC protein, harbors a dynamic bidirectional electrostatic network that connects the phenol pocket to two distal regions, namely the “G-hinge” and the “allosteric linker.” While the G-hinge influences the entry of phenol into the pocket, the allosteric linker passes the signal to the downstream ATPase domain. We show that phenol binding induces a rewiring of the electrostatic connections by eliciting dynamic allostery and demonstrates that perturbation of the core relay residues results in a complete loss of ATPase stimulation. Furthermore, we found a mutation of the G-hinge, ∼20 Å from the phenol pocket, promotes altered flexibility by shifting the pattern of conformational states accessed, leading to a protein with 7-fold enhanced phenol binding ability and enhanced transcriptional activation. Finally, we conducted a global analysis that illustrates that dynamic allostery-driven conserved community networks are universal and evolutionarily conserved across species. Taken together, these results provide insights into the mechanisms of dynamic allostery-mediated conformational changes in NtrC sensor proteins.

Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism

P-Rex (PI(3,4,5)P₃-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gβγ and PI(3,4,5)P₃ binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126° opening of the DH domain hinge helix. The off-axis position of Gβγ and PI(3,4,5)P₃ binding sites further suggests a counter-rotation of the P-Rex1 halves by 90° facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.

Cryo-EM, X-ray crystallography and crosslinking mass spectrometry are harnessed to solve the structure of the full-length Rho-GEF P-Rex1, uncovering a two-layered mechanism of autoinhibition released upon Gβγ and PI(3,4,5)P3 binding.

Pseudo Polyampholytes with Sensitively Ion-Responsive Conformational Transition Based on Positively Charged Host-Guest Complexes

Biological polyampholytes are ubiquitous in living organisms with primary functions including that serving as transporters for moving chemical molecular species across the cell membranes. Synthetic amphoteric macromolecules that can change their phase states depending on the environment to simulate some properties of natural polyampholytes are of great interests. Here, we explore implementation of synthetic pseudo polymeric ampholytes with ion-recognition-triggered conformational change. The phase transition behaviors of the ion-recognition-creative polyampholytes that containing deprotonated carboxylic acid groups as negative charges and 18-crown-6 units for forming positively charged host-guest complexes are systematically investigated. The ion-recognition-triggered phase transition behaviors of pseudo polyampholytes are significantly dependent on cation species and concentrations. Only those specific ions like K⁺ , Ba²⁺ , Sr²⁺ and Pb²⁺ ions that can form 1:1 host-guest complexes with 18-crown-6 units in polymers enable to control over the conformational change like that of the traditional pH-dependent polyampholytes. By regulating the content of the carboxylic acid groups to match the content of the ion-recognized positive charges provided by the host-guest complexes, the pseudo polyampholytes are more sensitive to the recognizable cations. Such ion-recognition-triggered amphoteric characteristics make the pseudo polyampholytes acting like biological proteins, nucleic acids and enzymes as molecular transporters, genetic code storage and biocatalysts in artificial systems. This article is protected by copyright. All rights reserved.

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

Ethylene-bridged oligoureas characterized by a continuous, switchable chain of hydrogen bonds and carrying a binding site (an N,N′-disubstituted urea) for a hydrogen-bond-accepting ligand (a phosphine oxide) were synthesized. These oligomers show stronger ligand binding when the binding site is located at the hydrogen-bond-donating terminus than when the same binding site is at the hydrogen-bond-accepting terminus. An acidic group at the terminus remote from the binding site allows hydrogen bond polarity, and hence ligand binding ability, to be controlled remotely by a deprotonation/reprotonation cycle. Addition of base induces a remote conformational change that is relayed through up to five urea linkages, reducing the ability of the binding site to retain an intermolecular association to its ligand, which is consequently released into solution. Reprotonation returns the polarity of the oligomer to its original directionality, restoring the function of the remote binding site, which consequently recaptures the ligand. This is the first example of a synthetic molecular structure that relays intermolecular binding information, and these “dynamic foldamer” structures are prototypes of components for chemical systems capable of controlling chemical function from a distance.

Switchable Zinc(II)-Responsive Globular β-Sheet Peptide

The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His₃-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pK_a of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.

Carbocation Footprinting of Soluble and Transmembrane Proteins

Here, we introduce carbocations (R3C+) as laser-initiated footprinting reagents for proteins. We screened seven candidates and selected trifluomethoxy benzyl bromide (TFBB) as an effective precursor for the electrophilic trifluomethoxy benzyl carbocation (TFB+) under laser (248 nm) irradiation on the fast photochemical oxidation of proteins (FPOP) platform. Initial results demonstrate that this electrophilic cation reagent affords residue coverage of nucleophilic amino acids including H, W, M, and S. Further, the addition of TFB+ increases the hydrophobicity of the peptides so that separation of isomeric peptide products by reversed-phase LC is improved, suggesting opportunities for subresidue footprinting. Comparison of apo- and holo-myoglobin footprints shows that the TFB+ footprinting is sensitive to protein conformational change and solvent accessibility. Interestingly, because the TFB+ is amphiphilic, the reagent can potentially footprint membrane proteins as demonstrated for vitamin K epoxide reductase (VKOR) stabilized in a micelle. Not only does footprinting of the extra-membrane domain occur, but also some footprinting of the hydrophobic transmembrane domain is achieved owing to the interaction of TFB+ with the micelle. Carbocation precursors are stable and amenable for tailoring their properties and those of the incipient carbocation, enabling targeting their soluble or membrane-associated or embedded regions and distinguishing between the extra- and trans-membrane domains of membrane proteins.

Identification and characterization of metamorphic proteins: Current and future perspectives

Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.

DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of DNA aptamers to interact with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and subsequent fusioning of the virus membrane with the host cell membrane. In order to achieve this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show, by means of state-of-the-art molecular simulations, that small DNA aptamers experimentally identified can recognize the S-protein of SARS-CoV-2, and characterize the details of the binding process. We find that their interaction with different subdomains of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby significantly reducing the probability of virus-cell binding. We provide evidence that, as a consequence, binding of the human ACE2 receptor may be crucially affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy.

A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern

A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.

Protein conformational switch discerned via network centrality properties

Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.

Dual Control of Peptide Conformation with Light and Metal Coordination

The design of a stimuli-responsive peptide whose conformation is controlled by wavelength-specific light and metal coordination is described. The peptide adopts a defined tertiary structure and its conformation can be modulated between an α-helical coiled coil and β-sheet. The peptide is designed with a hydrophobic interface to induce coiled coil formation and is based on a recently described strategy to obtain switchable helix dimers. Herein, we endowed the helix dimer with 8-hydroxyquinoline (HQ) groups to achieve metal coordination and shift to a β-sheet structure. It was found that the conformational shift only occurs upon introduction of Zn²⁺ ; other metal ions (Cu²⁺ , Fe³⁺ , Co²⁺ , Mg² , and Ni²⁺ ) do not offer switching likely due to non-specific metal-peptide coordination. A control peptide lacking the metal-coordinating residues does not show conformational switching with Zn²⁺ supporting the role of this metal in stabilizing the β-sheet conformation in a defined manner.

Lubricin as a tool for controlling adhesion in vivo and ex vivo

The ability to prevent or minimize the accumulation of unwanted biological materials on implantable medical devices is important in maintaining the long-term function of implants. To address this issue, there has been a focus on materials, both biological and synthetic, that have the potential to prevent device fouling. In this review, we introduce a glycoprotein called lubricin and report on its emergence as an effective antifouling coating material. We outline the versatility of lubricin coatings on different surfaces, describe the physical properties of its monolayer structures, and highlight its antifouling properties in improving implant compatibility as well as its use in treatment of ocular diseases and arthritis. This review further describes synthetic polymers mimicking the lubricin structure and function. We also discuss the potential future use of lubricin and its synthetic mimetics as antiadhesive biomaterials for therapeutic applications.

Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations

Recent research on fold-switching metamorphic proteins has revealed some notable exceptions to Anfinsen's hypothesis of protein folding. We have previously described how a single point mutation can enable a well-folded protein domain, one of the two PAS (Per-ARNT-Sim) domains of the human ARNT (aryl hydrocarbon receptor nuclear translocator) protein, to interconvert between two conformers related by a slip of an internal β-strand. Using this protein as a test case, we advance the concept of a "fragile fold," a protein fold that can reversibly rearrange into another fold that differs by a substantial number of hydrogen bonds, entailing reorganization of single secondary structure elements to more drastic changes seen in metamorphic proteins. Here we use a battery of biophysical tests to examine several factors affecting the equilibrium between the two conformations of the switching ARNT PAS-B Y456T protein. Of note, we find that factors which impact the HI loop preceding the shifted Iβ-strand affect both the equilibrium levels of the two conformers and the denatured state which links them in the interconversion process. Finally, we describe small molecules that selectively bind to and stabilize the wildtype conformation of ARNT PAS-B. These studies form a toolkit for studying fragile protein folds and could enable ways to modulate the biological functions of such fragile folds, both in natural and engineered proteins.

De novo design of a reversible phosphorylation-dependent switch for membrane targeting

Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells.

The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.

A pH-Induced Reversible Conformational Switch Able to Control the Photocurrent Efficiency in a Peptide Supramolecular System

External stimuli are potent tools that Nature uses to control protein function and activity. For instance, during viral entry and exit, pH variations are known to trigger large protein conformational changes. In Nature, also the electron transfer (ET) properties of ET proteins are influenced by pH-induced conformational changes. In this work, a pH-controlled, reversible 3₁₀ -helix to α-helix conversion (from acidic to highly basic pH values and vice versa) of a peptide supramolecular system built on a gold surface is described. The effect of pH on the ability of the peptide SAM to generate a photocurrent was investigated, with particular focus on the effect of the pH-induced conformational change on photocurrent efficiency. The films were characterized by electrochemical and spectroscopic techniques, and were found to be very stable over time, also in contact with a solution. They were also able to generate current under illumination, with an efficiency that is the highest recorded so far with biomolecular systems.

Volume and compressibility differences between protein conformations revealed by high-pressure NMR

Proteins often interconvert between different conformations in ways critical to their function. Although manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic +3 slip in the β-strand register as it switches between two stably folded conformations. Using high-pressure biomolecular NMR approaches, we obtained the first, to our knowledge, quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wild-type equivalent, and the interconversion proceeds through a chiefly unfolded intermediate state. Data collected in steady-state pressure and time-resolved pressure-jump modes, including observed pressure-dependent changes in the populations of the two conformers and increased rate of interconversion between conformers, support both hypotheses. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.

In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by the intracellular TLRs of humans

The coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has already resulted in a huge setback to mankind in terms of millions of deaths, while the unavailability of an appropriate therapeutic strategy has made the scenario much more severe. Toll-like receptors (TLRs) are crucial mediators and regulators of host immunity and the role of human cell surface TLRs in SARS-CoV-2 induced inflammatory pathogenesis has been demonstrated recently. However, the functional significance of the human intracellular TLRs including TLR3, 7, 8, and 9 is yet unclear. Hitherto, the involvement of these intracellular TLRs in inducing pro-inflammatory responses in COVID-19 has been reported but the identity of the interacting viral RNA molecule(s) and the corresponding TLRs have not been explored. This study hopes to rationalize the comparative binding of the major SARS-CoV-2 mRNAs to the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drives these interactions. Our in silico study on the binding of all mRNAs with the intracellular TLRs depicts that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are possible virus-associated molecular patterns that bind to TLR3, TLR9, and TLR7, respectively, and trigger downstream cascade reactions. Intriguingly, binding of the viral mRNAs resulted in variable degrees of conformational changes in the ligand-binding domain of the TLRs ratifying the activation of the downstream inflammatory signaling cascade. Taken together, the current study is the maiden report to describe the role of TLR3, 7, and 9 in COVID-19 immunobiology and these could serve as useful targets for the conception of a therapeutic strategy against the pandemic.

Engineered protein switches for exogenous control of gene expression

There is an ongoing need in the synthetic biology community for novel ways to regulate gene expression. Protein switches, which sense biological inputs and respond with functional outputs, represent one way to meet this need. Despite the fact that there is already a large pool of transcription factors and signaling proteins available, the pool of existing switches lacks the substrate specificities and activities required for certain applications. Therefore, a large number of techniques have been applied to engineer switches with novel properties. Here we discuss some of these techniques by broadly organizing them into three approaches. We show how novel switches can be created through mutagenesis, domain swapping, or domain insertion. We then briefly discuss their use as biosensors and in complex genetic circuits.

129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration

Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP "closed" conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.

Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers

Canonical proteins fold and function as conformational switches that toggle between their folded (on) and unfolded (off) states, a mechanism that also provides the basis for engineering transducers for biosensor applications. One of the limitations of such transducers, however, is their relatively narrow operational range, limited to ligand concentrations 20-fold below or above their C₅₀. Previously, we discovered that certain fast-folding proteins lose/gain structure gradually (downhill folding), which led us to postulate their operation as conformational rheostats capable of processing inputs/outputs in analog fashion. Conformational rheostats could make transducers with extended sensitivity. Here we investigate this hypothesis by engineering pH transducing into the naturally pH insensitive, downhill folding protein gpW. Particularly, we engineered histidine grafts into its hydrophobic core to induce unfolding via histidine ionization. We designed and tested the effects of ionization via computational modeling and studied experimentally the four most promising single grafts and two double grafts. All tested mutants become reversible pH transducers in the 4-9 range, and their response increases proportionally to how buried the histidine graft is. Importantly, the pH-dependent reversible (un)folding occurs in rheostatic fashion, so the engineered transducers can detect up to 6 orders of magnitude in [H⁺] for single grafts, and even more for double grafts. Our results demonstrate that downhill (un)folding coupled to binding produces the gradual, analog responses to the ligand (here H⁺) that are expected of conformational rheostats, and which make them a powerful mechanism for engineering transducers with sensitivity over many orders of magnitude in ligand concentration (broadband).