Well-defined Conformation Research Articles

FoldamerDB: a database of peptidic foldamers.

Foldamers are non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution. Since their first description about two decades ago, numerous studies have been undertaken dealing with the design, synthesis, characterization and application of foldamers. They have huge application potential as antimicrobial, anticancer and anti-HIV agents and in materials science. Despite their importance, there is no publicly available web resource providing comprehensive information on these compounds. Here we describe FoldamerDB, an open-source, fully annotated and manually curated database of peptidic foldamers. FoldamerDB holds the information about the sequence, structure and biological activities of the foldamer entries. It contains the information on over 1319 species and 1018 activities, collected from more than 160 research papers. The web-interface is designed to be clutter-free, user-friendly and it is compatible with devices of different screen sizes. The interface allows the user to search the database, browse and filter the foldamers using multiple criteria. It also offers a detailed help page to assist new users. FoldamerDB is hoped to bridge the gap in the freely available web-based resources on foldamers and will be of interest to diverse groups of scientists from chemists to biologists. The database can be accessed at http://foldamerdb.ttk.hu/.

Isolation, purification, and structural identification of a new bacteriocin made by Lactobacillus plantarum found in conventional kombucha

In recent years, the demand for “natural” products has increased, as customers prefer this type of product over those with added chemical preservatives. The critical issues associated with natural products are how to maintain their safety and quality as well as how to prolong their shelf life. In this study, Lactobacillus plantarum SLG10, isolated from kombucha (a traditional fermented drink in South China), produced a novel bacteriocin, SLG10, which was found to exert antibacterial activity on both Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. An innovative method, biochromatography coupled with reversed-phase high-performance liquid chromatography (RP-HPLC), was developed for the efficient screening and purification of the bacteriocin found in the cell-free suspension of L. plantarum SLG10. According to matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), the isolated bacteriocin had a molecular mass of 1422 Da. The amino acid sequence was Asn-Ile-Val-Trp-Gln-Leu-Ile-Gly-Leu-Pro-Ala-Gln-Al, as determined by N-sequencing. Bacteriocin SLG10 showed thermostability and pH tolerant characteristics and was sensitive to most proteases but not trypsin or pepsin. A well-defined linear conformation was suggested by circular dichroism (CD) spectroscopy and 3D structure predictions. The time-kill kinetics curve indicated that bacteriocin SLG10 was bactericidal. The antibacterial mechanism investigation revealed that bacteriocin SLG10 increased cell membrane permeability, causing potassium ion release. We also found that bacteriocin SLG10 can inhibit the formation of biofilms. These results suggest that bacteriocin SLG10 has a potential application in the food industry.

Ion Mobility Spectrometry of Macromolecules with Dipole Alignment Switchable by Varying the Gas Pressure.

Since inception in the 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) was implemented at or near the ambient gas pressure (AP). Recently, we developed FAIMS at 15-30 Torr within a mass spectrometer and demonstrated it for small and medium sized ions, including peptides. The overall separation properties mirrored those at AP, reflecting the shared underlying physics. Here we extend these analyses to macromolecules, namely, multiply charged proteins generated by electrospray ionization. The spectra for smaller proteins (ubiquitin, cytochrome c, myoglobin) again resemble those at AP, producing features for one or a few adjacent well-defined conformers with type C behavior. Large proteins (single aldolase domain and albumin) now follow, with no broad bands for type A or B species that dominated at 1 atm. Those unique behaviors were ascribed to pendular ions with electric dipoles reversibly locked by the strong field in FAIMS. Disappearance of those bands shows loss of alignment predicted by first-principles theory, further supporting dipole locking at AP. The capability to modulate dipole alignment by varying gas pressure at constant normalized field provides the basis for determining the ion dipole moment and direction within the molecular frame from the pressure of onset and characteristics of spectral drift. This new approach to alter FAIMS separations of proteins could make a powerful tool for structural biology and be useful for proteomics and imaging.

Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia

The Bac2A (RLARIVVIRVAR−NH2) is a linearized counterpart of cationic cyclic peptide Bactenecin—one of the smallest naturally occurring antimicrobial peptides (AMPs), which, however, generally exhibits a low or moderate antibacterial potency against gram-positive bacteria. Here, it is found that the Bac2A and its linear derivates cannot spontaneously fold into a well-defined helical conformation in solution, thus impairing the peptide amphipathicity and antibacterial activity. Hydrocarbon stapling is rationally designed to constrain the helical conformation of these linear peptides. Atomistic dynamics simulations reveal that the membrane-penetrating course of linear and stapled peptides include four distinct phases, during which the stapled peptides can maintain in an ordered helical conformation, while linear peptides are structured from intrinsic disorder in water solution to partially helical state in membrane interior, indicating that lipid environment can help the linear peptide refolding into amphipathic helix, although the refolding process would incur a large configurational entropy penalty. The antibacterial activities of the most potent stapled peptide are determined as MIC = 7.6 and 16 µg/ml against two gram-positive Staphylococcus aureus clinical strains isolated from pyemia. The activity values are improved by 7.1-fold and 5-fold as compared to that of native Bac2A peptide with MIC = 54 and 80 µg/ml, respectively.

Control of Excited-State Conformations in B,N-Acenes.

We present a new concept to control the conformations of molecules in the excited state through harvesting negative hyperconjugation. The strategy was realized with the 2,3,1,4-benzodiazadiborinane scaffold, which was prepared by a new synthetic procedure. Photochemical studies identified dual light emission, which was assigned to well-defined conformers. The emission at longer wavelength can be switched off by restricting the rotational degrees of freedom in the solid state as well as by controlling the energy levels of the excited states through adjusting the solvent polarity.

Secondary structures and cell-penetrating abilities of arginine-rich peptide foldamers

Foldamers, which are folded oligomers with well-defined conformations, have been recently reported to have a good cell-penetrating ability. α,α-Disubstituted α-amino acids are one such promising tool for the design of peptide foldamers. Here, we prepared four types of L-arginine-rich nonapeptides containing L-leucine or α,α-disubstituted α-amino acids, and evaluated their secondary structures and cell-penetrating abilities in order to elucidate a correlation between them. Peptides containing α,α-disubstituted α-amino acids had similar resistance to protease digestion but showed different secondary structures. Intracellular uptake assays revealed that the helicity of peptides was important for their cell-penetrating abilities. These findings suggested that a peptide foldamer with a stable helical structure could be promising for the design of cell-penetrating peptides.

Model peptide for anti-sigma factor domain HHCC zinc fingers: high reactivity toward 1O2 leads to domain unfolding.

All organisms have to cope with the deleterious effects of reactive oxygen species. Some of them are able to mount a transcriptional response to various oxidative stresses, which involves sensor proteins capable of assessing the redox status of the cell or to detect reactive oxygen species. In this article, we describe the design, synthesis and characterization of Zn·LASD(HHCC), a model for the Zn(Cys)2(His)2 zinc finger site of ChrR, a sensor protein involved in the bacterial defence against singlet oxygen that belongs to the family of zinc-binding anti-sigma factors possessing a characteristic H/C-X24/25-H-X3-C-X2-C motif. The 46-amino acid model peptide LASD(HHCC) was synthetized by solid phase peptide synthesis and its Zn2+-binding properties were investigated using electronic absorption, circular dichroism and NMR. LASD(HHCC) forms a 1 : 1 complex with Zn2+, namely Zn·LASD(HHCC), that adopts a well-defined conformation with the Zn2+ ion capping a 3-helix core that reproduces almost perfectly the fold of the ChrR in the vicinity of its zinc site. H2O2 reacts with Zn·LASD(HHCC) to yield a disulfide with a second order rate constant of 0.030 ± 0.002 M-1 s-1. Zn·LASD(HHCC) reacts rapidly with singlet oxygen to yield sulfinates and sulfonates. A lower limit of the chemical reaction rate constant between Zn·LASD(HHCC) and 1O2 was determined to be 3.9 × 106 M-1 s-1. Therefore, the Zn(Cys)2(His)2 site of Zn·LASD(HHCC) appears to be at least 5 times more reactive toward these two oxidants than that of a classical ββα zinc finger. Consequences for the activation mechanism of ChrR are discussed.

Control of conformation in α-helix mimicking aromatic oligoamide foldamers through interactions between adjacent side-chains.

The design, synthesis and structural characterization of non-natural oligomers that adopt well-defined conformations, so called foldamers, is a key objective in developing biomimetic 3D functional architectures. For the aromatic oligoamide foldamer family, use of interactions between side-chains to control conformation is underexplored. The current manuscript addresses this objective through the design, synthesis and conformational analyses of model dimers derived from 3-O-alkylated para-aminobenzoic acid monomers. The O-alkyl groups on these foldamers are capable of adopting syn- or anti-conformers through rotation around the Ar-CO/NH axes. In the syn-conformation this allows the foldamer to act as a topographical mimic of the α-helix whereby the O-alkyl groups mimic the spatial orientation of the i and i + 4 side-chains from the α-helix. Using molecular modelling and 2D NMR analyses, this work illustrates that covalent links and hydrogen-bonding interactions between side-chains can bias the conformation in favour of the α-helix mimicking syn-conformer, offering insight that may be more widely applied to control secondary structure in foldamers.

Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.

We have compiled an experimental data set (SWITCH10) of equilibrium constants for a series of hydrogen-bond-dependent conformational switches. These organic molecules possess common functionalities and are representative in terms of size and composition of systems routinely studied computationally. They exist as two well-defined conformations which serve as a useful tool to benchmark computational estimates of experimental Gibbs energy differences. We examine the performance of HF theory and a variety of density functionals (B3LYP, B3LYP-D3, CAM-B3LYP, ωB97X-D, M06-2X) against these experimental benchmarks. Surprisingly, despite a strong similarity between the two switch conformations, the average errors (0.4-1.7 kcal·mol-1) obtained across the data set for all methods are larger than obtained with HF calculations. B3LYP was found to outperform implicitly and explicitly dispersion-corrected functionals, with an average error smaller by 1 kcal·mol-1. Unsystematic errors in the optimized structures were found to contribute to the relatively poor performance obtained, while quasi-rigid rotor harmonic oscillator thermal contributions are important in improving the accuracy of computed Gibbs energy differences. These results emphasize the challenge of quantitative accuracy in computing solution-phase thermochemistry for flexible systems and caution against the often used (but unstated) assumption of favorable error cancellation in comparing conformers or stereoisomers.

Peptides as Bio-Inspired Electronic Materials: An Electrochemical and First-Principles Perspective.

Molecular electronics is at the forefront of interdisciplinary research, offering a significant extension of the capabilities of conventional silicon-based technology as well as providing a possible stand-alone alternative. Bio-inspired molecular electronics is a particularly intriguing paradigm, as charge transfer in proteins/peptides, for example, plays a critical role in the energy storage and conversion processes for all living organisms. However, the structure and conformation of even the simplest protein is extremely complex, and therefore, synthetic model peptides comprising well-defined geometry and predetermined functionality are ideal platforms to mimic nature for the elucidation of fundamental biological processes while also enhancing the design and development of single-peptide electronic components. In this Account, we first present intramolecular electron transfer within two synthetic peptides, one with a well-defined helical conformation and the other with a random geometry, using electrochemical techniques and computational simulations. This study reveals two definitive electron transfer pathways (mechanisms), the natures of which are dependent on secondary structure. Following on from this, electron transfer within a series of well-defined helical peptides, constrained by either Huisgen cycloaddition, ring-closing metathesis, or a lactam bridge, was determined. The electrochemical results indicate that each constrained peptide, in contrast to a linear counterpart, exhibits a remarkable shift of the formal potential to the positive (>460 mV) and a significant reduction of the electron transfer rate constant (up to 15-fold), which represent two distinct electronic "on/off" states. High-level calculations demonstrate that the additional backbone rigidity provided by the side-bridge constraints leads to an increased reorganization energy barrier, which impedes the vibrational fluctuations necessary for efficient intramolecular electron transfer through the peptide backbone. Further calculations reveal a clear mechanistic transition from hopping to superexchange (tunneling) stemming from side-bridge gating. We then extended our research to fine-tuning of the electronic properties of peptides through both structural and chemical manipulation, to reveal an interplay between electron-rich side chains and backbone rigidity on electron transfer. Further to this, we explored the possibility that the side-bridge constraints present in our synthetic peptides provide an additional electronic transport pathway, which led to the discovery of two distinct forms of quantum interferometer. The effects of destructive quantum interference appear essentially through both the backbone and an alternative tunneling pathway provided by the side bridge in the constrained β-strand peptide, as evidenced by a correlation between electrochemical measurements and conductance simulations for both linear and constrained β-strand peptides. In contrast, an interplay between quantum interference effects and vibrational fluctuations is revealed in the linear and constrained 310-helical peptides. Collectively, these exciting findings augment our fundamental knowledge of charge transfer dynamics and kinetics in peptides and also open up new avenues to design and develop functional bio-inspired electronic devices, such as on/off switches and quantum interferometers, for practical applications in molecular electronics.

Rationalizing Steroid Interactions with Lipid Membranes: Conformations, Partitioning, and Kinetics.

Steroids have numerous physiological functions associated with cellular signaling or modulation of the lipid membrane structure and dynamics, and as such, they have found broad pharmacological applications. Steroid–membrane interactions are relevant to multiple steps of steroid biosynthesis and action, as steroids are known to interact with neurotransmitter or membrane steroid receptors, and steroids must cross lipid membranes to exert their physiological functions. Therefore, rationalizing steroid function requires understanding of steroid–membrane interactions. We combined molecular dynamics simulations and isothermal titration calorimetry to characterize the conformations and the energetics of partitioning, in addition to the kinetics of flip–flop transitions and membrane exit, of 26 representative steroid compounds in a model lipid membrane. The steroid classes covered in this study include birth control and anabolic drugs, sex and corticosteroid hormones, neuroactive steroids, as well as steroids modulating the lipid membrane structure. We found that the conformational ensembles adopted by different steroids vary greatly, as quantified by their distributions of tilt angles and insertion depths into the membrane, ranging from well-defined steroid conformations with orientations either parallel or normal to the membrane, to wide conformational distributions. Surprisingly, despite their chemical diversity, the membrane/water partition coefficient is similar among most steroids, except for structural steroids such as cholesterol, leading to similar rates for exiting the membrane. By contrast, the rates of steroid flip–flop vary by at least 9 orders of magnitude, revealing that flip–flop is the rate-limiting step during cellular uptake of polar steroids. This study lays the ground for a quantitative understanding of steroid–membrane interactions, and it will hence be of use for studies of steroid biosynthesis and function as well as for the development and usage of steroids in a pharmacological context.

Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins

Intrinsically disordered regions are present in one-third of eukaryotic proteins and are overrepresented in cellular processes such as signaling, suggesting that intrinsically disordered proteins (IDPs) may have a functional advantage over folded proteins. Upon interacting with a partner macromolecule, a subset of IDPs can fold and bind to form a well-defined three-dimensional conformation. For example, disordered BH3-only proteins bind promiscuously to a large number of homologous BCL-2 family proteins, where they fold to a helical structure in a groove on the BCL-2–like protein surface. As two protein chains are involved in the folding reaction, and the structure is only formed in the presence of the partner macromolecule, this raises the question of where the folding information is encoded. Here, we examine these coupled folding and binding reactions to determine which component determines the folding and binding pathway. Using Φ value analysis to compare transition state interactions between the disordered BH3-only proteins PUMA and BID and the folded BCL-2–like proteins A1 and MCL-1, we found that, even though the BH3-only protein is disordered in isolation and requires a stabilizing partner to fold, its folding and binding pathway is encoded in the IDP itself; the reaction is not templated by the folded partner. We suggest that, by encoding both its transition state and level of residual structure, an IDP can evolve a specific kinetic profile, which could be a crucial functional advantage of disorder.

The True Catalyst Revealed: The Intervention of Chiral Ca and Mg Phosphates in Brønsted Acid Promoted Asymmetric Mannich Reactions

The acetylacetone-benzaldimine Mannich reaction catalyzed by Mg(II) and Ca(II) salts of chiral phosphoric acids (CPA) has been investigated computationally by QM/MM methods. Enantioselectivity in this reaction is both larger than and in the opposite sense to that observed for the same reaction catalyzed by the protic CPA catalyst alone. We present a mechanistic model from which the characteristic differences between these metal and metal-free catalysts, which can coexist in the same reaction mixture, can be understood. Alkaline earth salts with chiral phosphate counterions are found to be more catalytically active than the protic form, and the Ca(II) and Mg(II) CPA salts react via different mechanisms, with a higher coordination number favored by calcium over magnesium. In the well-ordered chiral cavities around these metal centers, asymmetric induction arises from the steric interaction with the imine protecting group in the unfavorable pathway, with both substrates adopting well-defined conformations. These mechanistic models have allowed us to rationalize the stereochemical outcome across a range of bimolecular reactions promoted by divalent metal phosphates formed with different CPAs.

Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1

P-glycoprotein, also known as multidrug resistance protein 1 or ABCB1, can export a wide range of chemically unrelated compounds, including chemotherapeutic drugs. ABCB1 consists of two transmembrane domains that form the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that energize substrate transport by ATP binding and hydrolysis. ATP binding triggers dimerization of the NBDs, which switches the transporter from an inward facing to an outward facing transmembrane domain conformation. We performed MD simulations to study the dynamic behavior of the NBD dimer in the presence or absence of nucleotides. In the apo configuration, the NBDs were overall attractive to each other as shown in the potential of mean force profile, but the energy well was shallow and broad. In contrast, a sharp and deep energy minimum (∼−42 kJ/mol) was found in the presence of ATP, leading to a well-defined conformation. Motif interaction network analyses revealed that ATP stabilizes the NBD dimer by serving as the central hub for interdomain connections. Simulations showed that forces promoting dimerization are multilayered, dominated by electrostatic interactions between the nucleotide and conserved amino acids of the signature sequence and the Walker A motif. In addition, direct and water-bridged hydrogen bonds between NBDs provided conformation-defining interactions. Importantly, we characterized a largely unrecognized but essential contribution from hydrophobic interactions between the adenine moiety of the nucleotides and a hydrophobic surface of the X-loop to the stabilization of the nucleotide-bound NBD dimer. These hydrophobic interactions lead to a sharp energy minimum, thereby conformationally restricting the nucleotide-bound state.

Purification, characterization and application of a novel antimicrobial peptide from Andrias davidianus blood.

This is the pioneer study on screening and isolation of antimicrobial peptide from the blood of Andrias davidianus. Here, we have developed a novel method by combining magnetic liposomes adsorption with reversed-phase high-performance liquid chromatography to purify and screen the antimicrobial peptides. From this screen, we identified a novel antimicrobial peptide which we name as andricin B. Andricin B is unique as it checks the growth of both Gram-positive and Gram-negative bacteria as well as few fungal species.

Structure analysis of the membrane-bound dermcidin-derived peptide SSL-25 from human sweat

SSL-25 (SSLLEKGLDGAKKAVGGLGKLGKDA) is one of the shortest peptides present in human sweat and is produced after the proteolytic processing of the parent peptide dermcidin. Both peptides are reported to have antimicrobial function. To determine the structure of SSL-25 in lipid bilayers, a series of 19F-labeled SSL-25 analogs were synthesized. Circular dichroism (CD) analysis showed that SSL-25 and all of its analogs formed α-helices in the presence of lipid vesicles, thus allowing a detailed analysis via oriented CD and solid-state NMR. The results suggest that SSL-25 resides on the membrane surface with a slight helix tilt angle. A detailed 19F NMR analysis revealed that SSL-25 does not form a continuous helix. The α-helical structure of the N-terminal part of the peptide was preserved in membranes of different lipid compositions and at various peptide-to-lipid molar ratios, but the C-terminus was disordered and did not fold into a well-defined α-helical conformation. Furthermore, the NMR results showed that SSL-25 resides on the membrane surface and does not re-orient into the membrane in response to changes in either peptide concentration or membrane composition. SSL-25 does not aggregate and remains fully mobile within the membrane bilayer, as shown by 19F NMR. SSL-25 has a high binding affinity toward bilayers mimicking bacterial lipid compositions, but does not bind to mammalian model membranes containing cholesterol. These observations may explain the selectivity of this peptide for bacterial membranes, and they are also in line with basic biophysical considerations on spontaneous lipid curvature and the general effect of cholesterol on peptide/lipid interactions.

Purification and characterization of plantaricin SLG1, a novel bacteriocin produced by Lb. plantarum isolated from yak cheese

Yak milk cheese is one of the most important foods for the Tibetan people. Lactobacillus plantarum SLG1 isolated from yak cheese was shown to produce a novel bacteriocin, plantaricin SLG1. Production of plantaricin SLG1 in MRS medium was maximized after 24 h incubation at 37 °C (the stationary phase of growth). An innovative method, namely magnetic liposome adsorption combined with reversed-phase high performance liquid chromatography (RP-HPLC), was developed to screen for and efficiently purify bacteriocin compounds from the cell free supernatants from Lb. plantarum SLG1. The molecular mass of plantaricin SLG1 is 1083.25 Da and its amino acid sequence Tyr-Gly-Asn-Gly-Val-Phe-Ser-Val-Ile-Lys was determined by N-sequencing. Analyses by Circular dichroism (CD) spectra and predicted 3D structure suggested that the peptide maintains a well-defined conformation. Plantaricin SLG1 exhibited a wide range of antimicrobial activity against many food-borne spoilage and pathogenic bacteria, as well as some fungi. Results using scanning electron microscopy indicated that the mode of action was bactericidal and plantaricin SLG1 was able to damage the cell membrane integrity ultimately causing pathogen lethality.

A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis.

Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach.

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular molecules sometimes alter the energy landscape, thereby changing the ensemble of likely low-energy conformations. The effects of these energy landscape changes on the conformational ensemble are particularly challenging to visualize for large RNAs. We have created a robust approach for visualizing the conformational ensemble of RNAs that is well suited for in vitro versus in vivo comparisons. Our method creates a stable map of conformational space for a given RNA sequence. We first identify single point mutations in the RNA that maximally sample suboptimal conformational space based on the ensemble’s partition function. Then, we cluster these diverse ensembles to identify the most diverse partition functions for Boltzmann stochastic sampling. By using, to our knowledge, a novel nestedness distance metric, we iteratively add mutant suboptimal ensembles to converge on a stable 2D map of conformational space. We then compute the selective 2′ hydroxyl acylation by primer extension (SHAPE)-directed ensemble for the RNA folding under different conditions, and we project these ensembles on the map to visualize. To validate our approach, we established a conformational map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures. In the presence of adenine, projection of the SHAPE-directed sampling correctly identified the on-conformation; without the ligand, only off-conformations were visualized. We also collected the whole-transcript in vitro and in vivo SHAPE-MaP for human β-actin messenger RNA that revealed similar global folds in both conditions. Nonetheless, a comparison of in vitro and in vivo data revealed that specific regions exhibited significantly different SHAPE-MaP profiles indicative of structural rearrangements, including rearrangement consistent with binding of the zipcode protein in a region distal to the stop codon.

Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein

The exact function of human gasdermin-B (GSDMB), which regulates differentiation and growth of epithelial cells, is yet to be elucidated. In human epidermal growth factor receptor 2 (HER2)-positive breast cancer, GSDMB gene amplification and protein overexpression indicate a poor response to HER2-targeted therapy. Genome-wide association studies revealed a correlation between GSDMB SNPs and an increased susceptibility to Crohn's disease, ulcerative colitis, and asthma. The N- and C-terminal domains of all gasdermins possess lipid-binding and regulatory activities, respectively. Inflammatory caspases cleave gasdermin-D in the interdomain linker but not GSDMB. The cleaved N-terminal domain binds phosphoinositides and cardiolipin, forms membrane-disrupting pores, and executes pyroptosis. We show that both full-length GSDMB and the N-terminal domain bind to nitrocellulose membranes immobilized with phosphoinositides or sulfatide, but not with cardiolipin. In addition, the GSDMB N-terminal domain binds liposomes containing sulfatide. The crystal structure of the GSDMB C-terminal domain reveals the structural impact of the amino acids encoded by SNPs that are linked to asthma and inflammatory bowel disease (IBD). A loop that carries the polymorphism amino acids corresponding to healthy individuals (Gly299:Pro306) exhibits high conformational flexibility, whereas the loop carrying amino acids found in individuals with increased disease risk (Arg299:Ser306) exhibits a well-defined conformation and higher positive surface charge. Apoptotic executioner caspase-3, -6, and -7, but not the inflammatory caspases, cleave GSDMB at 88DNVD91 within the N-terminal domain. Selective sulfatide binding may indicate possible function for GSDMB in the cellular sulfatide transport.