Helical Interface Research Articles

Topological interface and corner states of flexural waves in metamaterial plates with glide-symmetric holes

This study investigates the topological localization and propagation of flexural waves in metamaterial plates with perforated holes exhibiting glide symmetry. The dispersion relations of flexural waves in this mechanical system exhibit four-fold Dirac degeneracies at the M point of the Brillouin zone. By properly adjusting the rotation angles of the perforated holes, these degeneracies can be lifted up to create omnidirectional bandgaps, enabling nontrivial topological phases. Both numerical and experimental results demonstrate multiple topological states of flexural waves in the developed elastic metaplates, including dual-band helical interface states and anisotropic interface/corner states. The simple perforated metaplates with glide-symmetric holes provide novel, manufacturable platforms for the flexible manipulation of topological flexural waves, greatly facilitating potential applications such as energy harvesting and signal enhancement.

Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs).

Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.

Abstract 1025: Structural Basis Of Apolipoprotein A1 Activation Of Lecithin:Cholesterol Acyl Transferase In High Density Lipoproteins

Lecithin:cholesterol acyl transferase (LCAT) is responsible for the formation of extracellular cholesteryl ester, which is critical for high density lipoprotein (HDL) maturation. It also modulates numerous HDL physiological functions by impacting particle subspeciation patterns. LCAT is activated by apolipoprotein A1 (APOA1) which forms antiparallel dimers around the edge of nascent HDL. Previous work has suggested that the interface of APOA1 helices 4 and 6, when properly aligned, creates two symmetrical sites for productive LCAT binding. Size exclusion chromatography was used to isolate reconstituted HDL discs containing two molecules of APOA1 chemically crosslinked to 2 LCAT molecules. Mass spectrometry using multiple crosslinkers, including a novel application of formaldehyde, indicated that LCAT interacts with both APOA1 helices 4 and 6. Cryo-electron microscopy (cryoEM) was used to determine a 10 Å structure of the complex. Using the HADDOCK suite of molecular docking tools, we developed a structural model of LCAT bound to APOA1 discs that is consistent with the preponderance of data accumulated so far. The model shows that LCAT may bind at the two symmetrical sites in different orientations, possibly reflecting different steps of the LCAT reaction. Work to improve the resolution of the cryoEM datasets is ongoing. Further work, using strategically designed cysteine mutations in APOA1 to lock helices 4 and 6 together, suggests that the helices do not move apart during the LCAT reaction process. Determination of the structural interactions between LCAT and its activator, APOA1, is crucial to understanding HDL maturation, which has significant clinical implications. This work provides the highest resolution structural model available for this important interaction.

Experimental and computational investigation of the effect of Hsc70 structural variants on inhibiting amylin aggregation

The misfolding and aggregation of human islet amyloid polypeptide (hIAPP), also known as amylin, have been implicated in the pathogenesis of type 2 diabetes (T2D). Heat shock proteins, specifically, heat shock cognate 70 (Hsc70), are molecular chaperones that protect against hIAPP misfolding and inhibits its aggregation. Nevertheless, there is an incomplete understanding of the mechanistic interactions between Hsc70 domains and hIAPP, thus limiting their potential therapeutic role in diabetes. This study investigates the inhibitory capacities of different Hsc70 variants, aiming to identify the structural determinants that strike a balance between efficacy and cytotoxicity. Our experimental findings demonstrate that the ATPase activity of Hsc70 is not a pivotal factor for inhibiting hIAPP misfolding. We underscore the significance of the C-terminal substrate-binding domain of Hsc70 in inhibiting hIAPP aggregation, emphasizing that the removal of the lid subdomain diminishes the inhibitory effect of Hsc70. Additionally, we employed atomistic discrete molecular dynamics simulations to gain deeper insights into the interaction between Hsc70 variants and hIAPP. Integrating both experimental and computational findings, we propose a mechanism by which Hsc70's interaction with hIAPP monomers disrupts protein-protein connections, primarily by shielding the β-sheet edges of the Hsc70-β-sandwich. The distinctive conformational dynamics of the alpha helices of Hsc70 potentially enhance hIAPP binding by obstructing the exposed edges of the β-sandwich, particularly at the β5-β8 region along the alpha helix interface. This, in turn, inhibits fibril growth, and similar results were observed following hIAPP dimerization. Overall, this study elucidates the structural intricacies of Hsc70 crucial for impeding hIAPP aggregation, improving our understanding of the potential anti-aggregative properties of molecular chaperones in diabetes treatment.

Dual-Capped Helical Interface Mimics.

Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.

Dual-polarization helical interface states in inverse-designed photonic crystals with glide symmetry

Dual-polarization helical interface states in inverse-designed photonic crystals with glide symmetry

Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR.

Single-span oligomeric α-helical transmembrane proteins are common in virus ion channels, which are targets of antiviral drugs. Knowledge about the high-resolution structures of these oligomeric α-helical bundles is so far scarce. Structure determination of these membrane proteins by solid-state NMR traditionally requires resolving and assigning protein chemical shifts and measuring many interhelical distances, which are time-consuming. To accelerate experimental structure determination, here we introduce a simple solid-state NMR approach that uses magnetization transfer from water and lipid protons to the protein. By detecting the water- and lipid-transferred intensities of the high-sensitivity methyl 13C signals of Leu, Val, and Ile residues, which are highly enriched in these membrane proteins, we can derive models of the topology of these homo-oligomeric helical bundles. The topology is specified by the positions of amino acid residues in heptad repeats and the orientations of residues relative to the channel pore, lipids, and the helical interface. We demonstrate this water- and lipid-edited methyl NMR approach on the envelope (E) protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. We show that water-edited and lipid-edited 2D 13C-13C correlation spectra can be measured with sufficient sensitivity. Even without resolving multiple residues of the same type in the NMR spectra, we can obtain the helical bundle topology. We apply these experiments to the structurally unknown E proteins of the MERS coronavirus and the human coronavirus NL63. The resulting structural topologies show interesting differences in the positions of the aromatic residues in these three E proteins, suggesting that these viroporins may have different mechanisms of activation and ion conduction.

Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8

Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loopwith the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.

Topological photonic crystal fiber with honeycomb structure.

We analyze a new type of photonic crystal fiber which consists of the core and cladding that distinct in topology by tuning the position of air holes in each hexagonal unit cell where the C6v symmetry is respected. The p-d band inversion between the core and cladding leads to topological interface modes inside the band gap, which can propagate along the fiber with a nonzero momentum in perpendicular to the corss section of a fiber. The helical topological interface modes possess the pseudospin-momentum locking effect inherited from the corresonding two-dimensional photonic crystal characterized by the Z2 topology. The wave functions for the topological interface modes are analytically studied and compared successfully to the numerical results, enlighting a novel way to use photonic crystal fiber to transfer information.

The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate.

Class 1 cytokine receptors transmit signals through the membrane by a single transmembrane helix to an intrinsically disordered cytoplasmic domain that lacks kinase activity. While specific binding to phosphoinositides has been reported for the prolactin receptor (PRLR), the role of lipids in PRLR signaling is unclear. Using an integrative approach combining nuclear magnetic resonance spectroscopy, cellular signaling experiments, computational modeling, and simulation, we demonstrate co-structure formation of the disordered intracellular domain of the human PRLR, the membrane constituent phosphoinositide-4,5-bisphosphate (PI(4,5)P2) and the FERM-SH2 domain of the Janus kinase 2 (JAK2). We find that the complex leads to accumulation of PI(4,5)P2 at the transmembrane helix interface and that the mutation of residues identified to interact specifically with PI(4,5)P2 negatively affects PRLR-mediated activation of signal transducer and activator of transcription 5 (STAT5). Facilitated by co-structure formation, the membrane-proximal disordered region arranges into an extended structure. We suggest that the co-structure formed between PRLR, JAK2, and PI(4,5)P2 locks the juxtamembrane disordered domain of the PRLR in an extended structure, enabling signal relay from the extracellular to the intracellular domain upon ligand binding. We find that the co-structure exists in different states which we speculate could be relevant for turning signaling on and off. Similar co-structures may be relevant for other non-receptor tyrosine kinases and their receptors.

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222.

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at 45 positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length.

Bicyclic Schellman Loop Mimics (BSMs): Rigid Synthetic C-Caps for Enforcing Peptide Helicity.

Macrocyclic peptides are the prevalent way to mimic interface helices for disruption of protein interactions, but current strategies to do this via synthetic C-cap mimics are underdeveloped and suboptimal. Bioinformatic studies described here were undertaken to better understand Schellman loops, the most common C-caps in proteins, to design superior synthetic mimics. An algorithm (Schellman Loop Finder) was developed, and data mining with this led to the discovery that these secondary structures are often stabilized by combinations of three hydrophobic side chains, most frequently from Leu, to form hydrophobic triangles. That insight facilitated design of synthetic mimics, bicyclic Schellman loop mimics (BSMs), where the hydrophobic triumvirate was replaced by 1,3,5-trimethylbenzene. We demonstrate that BSMs can be made quickly and efficiently, and are more rigid and helix-inducing than the best current C-cap mimics, which are rare and all monocycles.

Neutron Reflectometry and Molecular Simulations Demonstrate HIV-1 Nef Homodimer Formation on Model Lipid Bilayers

The HIV-1 Nef protein plays a critical role in viral infectivity, high-titer replication in vivo, and immune escape of HIV-infected cells. Nef lacks intrinsic biochemical activity, functioning instead through interactions with diverse host cell signaling proteins and intracellular trafficking pathways. Previous studies have established an essential role for Nef homodimer formation at the plasma membrane for most if not all its functions. Here we combined neutron reflectometry of full-length myristoylated Nef bound to model lipid bilayers with molecular simulations based on previous X-ray crystal structures of Nef homodimers. This integrated approach provides direct evidence that Nef associates with the membrane as a homodimer with its structured core region displaced from the membrane for partner protein engagement. Parallel studies of a dimerization-defective mutant, Nef-L112D, demonstrate that the helical dimerization interface present in previous crystal structures stabilizes the membrane-bound dimer. X-ray crystallography of the Nef-L112D mutant in complex with the SH3 domain of the Nef-associated host cell kinase Hck revealed a monomeric 1:1 complex instead of the 2:2 dimer complex formed with wild-type Nef. Importantly, the crystal structure of the Nef-L112D core and SH3 interface are virtually identical to the wild-type complex, indicating that this mutation does not affect the overall Nef fold. These findings support the intrinsic capacity of Nef to homodimerize at lipid bilayers using structural features present in X-ray crystal structures of dimeric complexes.

The open structure of a neonatal diabetes-causing variant of the pancreatic KATP channel determined using cryo-electron microscopy.

Pancreatic ATP-sensitive potassium (KATP) channels, comprising four Kir6.2 and four SUR1 subunits, control insulin secretion in β-cells by coupling glucose metabolism with membrane excitability. Regulation of KATP channels involves orchestrated interactions of their subunits, Kir6.2 and SUR1, and ligands. ATP and PIP2 are known to inhibit and stimulate channel activity, respectively. Although Kir6.2 harbors the primary binding sites for ATP and PIP2, SUR1 is required to confer high channel sensitivity to both ligands. Mutations in channel proteins that disrupt ATP and PIP2 gating cause insulin secretion disease. Kir6.2-Q52R is a neonatal diabetes mutation that results in channels with extremely high open probability and low ATP sensitivity. Previous studies suggest the Kir6.2-Q52R mutation stabilizes channel opening in a SUR1-dependent manner, but the structural mechanism is unknown. Here, we determined the cryoEM structure of the Kir6.2-Q52R4SUR14 channel in the absence of nucleotides or pharmacological ligands. This 3.3 Å resolution structure reveals that Kir6.2 is open, with its cytoplasmic domain (CTD) corkscrewed up to the membrane. The side-chain of Kir6.2-Q52R is flipped away from the ATP-binding site and embedded into SUR1-TMD0 in a cation-pi interaction with SUR1-W51 at the membrane. The cryo-EM map has clear density showing the first intracellular loop of SUR1-TMD0 (ICL1, 52-60) is ordered and forms main chain interactions between Kir6.2-βA (the CTD β-strand just N-terminal to the interfacial helix) and SUR1-ICL1, tethering the CTD to TMD0 to stabilize the open state. Our study provides structural insights into the mechanism by which the Kir6.2-Q52R mutation causes severe neonatal diabetes and how Kir6.2 and SUR1 interact to stabilize KATP channels in the open state.

Allosteric inhibition via nonpolar terpenoid inhibitors.

Protein tyrosine phosphatases (PTPs) are promising drug targets for treating a wide range of diseases such as diabetes, cancer, and neurological disorders, but their conserved active sites have complicated the design of selective therapeutics. This study examines the allosteric inhibition of PTP1B by amorphadiene (AD) and α-bisabolene(AB), terpenoid hydrocarbons that are unusually selective inhibitors. Molecular dynamics (MD) simulations carried out in this study suggest that both AD and AB can stably sample multiple neighboring sites on the allosterically influential C-terminus of the catalytic domain. Intriguingly, the binding mode of AD and AB differs from that of the most well-studied allosteric inhibitor of PTP1B, BBR. Indeed, biophysical measurements and MD simulations indicate that AD and BBR can bind simultaneously. Upon binding, both inhibitors destabilize the α7 helix and disrupt hydrogen bonds that facilitate closure of the catalytically essential WPD loop. The α7 helix is destabilized through the significant disruption of localized interactions at the α3-α7 helix interface for AD, AB, and BBR. Additionally, our findings suggest that the selectivity of AD and AB to PTP1B over TCPTP is due to relatively small differences in the composition of the α7 which eliminate the hydrophobic pocket in which the ligands bind to PTP1B. These findings indicate that AD and AB may be promising scaffolds for building allosteric inhibitors of PTP1B and illustrate more broadly how unfunctionalized terpenoids can engage in specific interactions with protein surfaces.

Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer.

The impact of Lys28 acetylation on Alzheimer's Aβ peptide binding to the lipid bilayer has not been previously studied, either experimentally or computationally. To probe this common post-translational modification, we performed all-atom replica exchange molecular dynamics simulations targeting binding and aggregation of acetylated acAβ25-35 peptide within the DMPC bilayer. Using the unmodified Aβ25-35 studied previously as a reference, our results can be summarized as follows. First, Lys28 acetylation strengthens the Aβ25-35 hydrophobic moment and consequently promotes the helical structure across the peptide extending it into the N-terminus. Second, because Lys28 acetylation disrupts electrostatic contact between Lys28 and lipid phosphate groups, it reduces the binding affinity of acAβ25-35 peptides to the DMPC bilayer. Accordingly, although acetylation preserves the bimodal binding featuring a preferred inserted state and a less probable surface bound state, it decreases the stability of the former. Third, acetylation promotes acAβ25-35 aggregation and eliminates monomers as thermodynamically viable species. More importantly, acAβ25-35 retains as the most thermodynamically stable the inserted dimer with unique head-to-tail helical aggregation interface. However, due to enhanced helix structure, this dimer state becomes less stable and is less likely to propagate into higher order aggregates. Thus, acetylation is predicted to facilitate the formation of low-molecular-weight oligomers. Other post-translational modifications, including phosphorylation and oxidation, reduce helical propensity and have divergent impact on aggregation. Consequently, acetylation, when considered in its totality, has distinct consequences on Aβ25-35 binding and aggregation in the lipid bilayer.

Topological examination of the bacteriophage lambda S holin by EPR spectroscopy

The S protein from bacteriophage lambda is a three-helix transmembrane protein produced by the prophage which accumulates in the host membrane during late gene expression. It is responsible for the first step in lysing the host cell at the end of the viral life cycle by multimerizing together to form large pores which permeabilize the host membrane to allow the escape of virions. Several previous studies have established a model for the assembly of holin into functional holes and the manner in which they pack together, but it is still not fully understood how the very rapid transition from monomer or dimer to multimeric pore occurs with such precise timing once the requisite threshold is reached. Here, site-directed spin labeling with a nitroxide label at introduced cysteine residues is used to corroborate existing topological data from a crosslinking study of the multimerized holin by EPR spectroscopy. CW-EPR spectral lineshape analysis and power saturation data are consistent with a three-helix topology with an unstructured C-terminal domain, as well as at least one interface on transmembrane domain 1 which is exposed to the lumen of the hole, and a highly constrained steric environment suggestive of a tight helical packing interface at transmembrane domain 2.

Voltage-sensor movements in the Eag Kv channel under an applied electric field

Voltage-dependent ion channels regulate the opening of their pores by sensing the membrane voltage. This process underlies the propagation of action potentials and other forms of electrical activity in cells. The voltage dependence of these channels is governed by the transmembrane displacement of the positive charged S4 helix within their voltage-sensor domains. We use cryo-electron microscopy to visualize this movement in the mammalian Eag voltage-dependent potassium channel in lipid membrane vesicles with a voltage difference across the membrane. Multiple structural configurations show that the applied electric field displaces S4 toward the cytoplasm by two helical turns, resulting in an extended interfacial helix near the inner membrane leaflet. The position of S4 in this down conformation is sterically incompatible with an open pore, thus explaining how movement of the voltage sensor at hyperpolarizing membrane voltages locks the pore shut in this kind of voltage-dependent K+ (Kv) channel. The structures solved in lipid bilayer vesicles detail the intricate interplay between Kv channels and membranes, from showing how arginines are stabilized deep within the membrane and near phospholipid headgroups, to demonstrating how the channel reshapes the inner leaflet of the membrane itself.

Engineering Peptide Inhibitors of the HFE-Transferrin Receptor 1 Complex.

The protein HFE (homeostatic iron regulator) is a key regulator of iron metabolism, and mutations in HFE underlie the most frequent form of hereditary haemochromatosis (HH-type I). Studies have shown that HFE interacts with transferrin receptor 1 (TFR1), a homodimeric type II transmembrane glycoprotein that is responsible for the cellular uptake of iron via iron-loaded transferrin (holo-transferrin) binding. It has been hypothesised that the HFE/TFR1 interaction serves as a sensor to the level of iron-loaded transferrin in circulation by means of a competition mechanism between HFE and iron-loaded transferrin association with TFR1. To investigate this, a series of peptides based on the helical binding interface between HFE and TFR1 were generated and shown to significantly interfere with the HFE/TFR1 interaction in an in vitro proximity ligation assay. The helical conformation of one of these peptides, corresponding to the α1 and α2 helices of HFE, was stabilised by the introduction of sidechain lactam “staples”, but this did not result in an increase in the ability of the peptide to disrupt the HFE/TFR1 interaction. These peptides inhibitors of the protein–protein interaction between HFE and TFR1 are potentially useful tools for the analysis of the functional role of HFE in the regulation of hepcidin expression.

Robust all-electrical topological valley filtering using monolayer 2D-Xenes

We propose a realizable device design for an all-electrical robust valley filter that utilizes spin protected topological interface states hosted on monolayer 2D-Xene materials with large intrinsic spin–orbit coupling. In contrast with conventional quantum spin-Hall edge states localized around the X-points, the interface states appearing at the domain wall between topologically distinct phases are either from the K or K^{prime} points, making them suitable prospects for serving as valley-polarized channels. We show that the presence of a large band-gap quantum spin-Hall effect enables the spatial separation of the spin–valley locked helical interface states with the valley states being protected by spin conservation, leading to robustness against short-range nonmagnetic disorder. By adopting the scattering matrix formalism on a suitably designed device structure, valley-resolved transport in the presence of nonmagnetic short-range disorder for different 2D-Xene materials is also analyzed in detail. Our numerical simulations confirm the role of spin–orbit coupling in achieving an improved valley filter performance with a perfect quantum of conductance attributed to the topologically protected interface states. Our analysis further elaborates clearly the right choice of material, device geometry and other factors that need to be considered while designing an optimized valleytronic filter device.