Key residues in the VDAC2-BAK complex can be targeted to modulate apoptosis.

BAK and BAX execute intrinsic apoptosis by permeabilising the mitochondrial outer membrane. Their activity is regulated through interactions with pro-survival BCL-2 family proteins and with non-BCL-2 proteins including the mitochondrial porin VDAC2. VDAC2 is important for bringing both BAK and BAX to mitochondria where they execute their apoptotic function. Despite this important function in apoptosis, while interactions with pro-survival family members are well characterised and have culminated in the development of drugs that target these interfaces to induce cancer cell apoptosis, the interaction between BAK and VDAC2 remains largely undefined. Deep scanning mutagenesis coupled with cysteine linkage identified key residues in the interaction between BAK and VDAC2. Obstructive labelling of specific residues in the BH3 domain or hydrophobic groove of BAK disrupted this interaction. Conversely, mutating specific residues in a cytosol-exposed region of VDAC2 stabilised the interaction with BAK and inhibited BAK apoptotic activity. Thus, this VDAC2-BAK interaction site can potentially be targeted to either inhibit BAK-mediated apoptosis in scenarios where excessive apoptosis contributes to disease or to promote BAK-mediated apoptosis for cancer therapy.

Mechanical activation opens a lipid-lined pore in OSCA ion channels.

OSCA/TMEM63 channels are the largest known family of mechanosensitive channels1-3, playing critical roles in plant4-7 and mammalian8,9 mechanotransduction. Here we determined 44 cryogenic electron microscopy structures of OSCA/TMEM63 channels in different environments to investigate the molecular basis of OSCA/TMEM63 channel mechanosensitivity. In nanodiscs, we mimicked increased membrane tension and observed a dilated pore with membrane access in one of the OSCA1.2 subunits. In liposomes, we captured the fully open structure of OSCA1.2 in the inside-in orientation, in which the pore shows a large lateral opening to the membrane. Unusually for ion channels, structural, functional and computational evidence supports the existence of a 'proteo-lipidic pore' in which lipids act as a wall of the ion permeation pathway. In the less tension-sensitive homologue OSCA3.1, we identified an 'interlocking' lipid tightly bound in the central cleft, keeping the channel closed. Mutation of the lipid-coordinating residues induced OSCA3.1 activation, revealing a conserved open conformation of OSCA channels. Our structures provide a global picture of the OSCA channel gating cycle, uncover the importance of bound lipids and show that each subunit can open independently. This expands both our understanding of channel-mediated mechanotransduction and channel pore formation, with important mechanistic implications for the TMEM16 and TMC protein families.

Graphene exfoliation using multidomain peptides.

Liquid-phase exfoliation using biomolecules in aqueous solution is a promising approach to obtain high quality 2D nanosheets. For example, the well-studied graphene-binding peptide, P1 (sequence HSSYWYAFNNKT), has been previously investigated and shown to have a good ability to exfoliate graphene sheets in aqueous conditions under sonication, maintaining colloidal stability. Building on this, the biomolecular exfoliant and assembly motif (BEAM) peptide, that features a graphene-binding domain at one end and a hexagonal boron nitride (h-BN) binding domain at the other, separated by a 10-carbon fatty acid chain in the centre, is shown to exfoliate graphene sheets from bulk graphite in aqueous media. An in-depth examination of the ability of the BEAM to both facilitate sheet exfoliation under sonication conditions and also maintain colliodal stability is provided through molecular dynamics simulations. These findings open new possibilities for designing multi-functional molecules that can both exfoliate and organise 2D materials into heterostructures under ambient conditions in aqueous media.

The functional evolution of architecturally different plant geranyl diphosphate synthases from geranylgeranyl diphosphate synthase.

Terpenoids constitute the largest class of plant primary and secondary metabolites with a broad range of biological and ecological functions. They are synthesized from isopentenyl diphosphate and dimethylallyl diphosphate, which in plastids are condensed by geranylgeranyl diphosphate synthases (GGPPSs) to produce GGPP (C20) for diterpene biosynthesis and by geranyl diphosphate synthases (GPPSs) to form GPP (C10) for monoterpene production. Depending on the plant species, unlike homomeric GGPPSs, GPPSs exist as homo- and heteromers, the latter of which contain catalytically inactive GGPPS-homologous small subunits (SSUs) that can interact with GGPPSs. By combining phylogenetic analysis with functional characterization of GGPPS homologs from a wide range of photosynthetic organisms, we investigated how different GPPS architectures have evolved within the GGPPS protein family. Our results reveal that GGPPS gene family expansion and functional divergence began early in nonvascular plants, and that independent parallel evolutionary processes gave rise to homomeric and heteromeric GPPSs. By site-directed mutagenesis and molecular dynamics simulations, we also discovered that Leu-Val/Val-Ala pairs of amino acid residues were pivotal in the functional divergence of homomeric GPPSs and GGPPSs. Overall, our study elucidated an evolutionary path for the formation of GPPSs with different architectures from GGPPSs and uncovered the molecular mechanisms involved in this differentiation.

Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures.

Assembling nanoparticles (NPs) into well-defined superstructures can lead to emergent collective properties that depend on their 3-D structural arrangement. Peptide conjugate molecules designed to both bind to NP surfaces and direct NP assembly have proven useful for constructing NP superstructures, and atomic- and molecular-level alterations to these conjugates have been shown to manifest in observable changes to nanoscale structure and properties. The divalent peptide conjugate, C16-(PEPAu)2 (PEPAu = AYSSGAPPMPPF), directs the formation of one-dimensional helical Au NP superstructures. This study examines how variation of the ninth amino acid residue (M), which is known to be a key Au anchoring residue, affects the structure of the helical assemblies. A series of conjugates of differential Au binding affinities based on variation of the ninth residue were designed, and Replica Exchange with Solute Tempering (REST) Molecular Dynamics simulations of the peptides on an Au(111) surface were performed to determine the approximate surface contact and to assign a binding score for each new peptide. A helical structure transition from double helices to single helices is observed as the peptide binding affinity to the Au(111) surface decreases. Accompanying this distinct structural transition is the emergence of a plasmonic chiroptical signal. REST-MD simulations were also used to predict new peptide conjugate molecules that would preferentially direct the formation of single-helical AuNP superstructures. Significantly, these findings demonstrate how small modifications to peptide precursors can be leveraged to precisely direct inorganic NP structure and assembly at the nano- and microscale, further expanding and enriching the peptide-based molecular toolkit for controlling NP superstructure assembly and properties.

Achieving regioselective materials binding using multidomain peptides.

The ability to integrate two disparate materials-binding domains into a single ligand to achieve regiospecific binding would be powerful to direct material assembly; however, this has proven challenging to achieve due to cross-materials binding. Accomplishing this goal might be achieved by harnessing the precision of biology to exploit the recognition between peptides and specific nanomaterials. Here, a designed bifunctional molecule termed Biomolecular Exfoliant and Assembly Motifs (BEAM) is introduced, featuring two different materials-binding peptide domains, one for graphene and one for hexagonal boron nitride (h-BN), at each end of the molecule, separated by a fatty acid spacer. The BEAM is demonstrated to bind strongly to both graphene and h-BN surfaces, and in each case the materials-binding peptide domain is shown to preferentially bind its target material. Critically, the two materials-binding domains exhibited limited cross-domain interaction. The BEAM design concept shows substantial potential to eventually guide self-organization of a range of materials in aqueous media.

Manipulation of peptide-fatty acid bioconjugates on graphene: effects of fatty acid chain length and attachment point.

The non-destructive functionalisation of graphene in aqueous media is a critical process with the potential to enhance the versatility of the 2D nanosheet material as a technological enabler. This could also unlock strategies for a wider uptake of graphene in bio-related applications. Graphene functionalisation can be achieved using peptides that specifically recognise the carbon-based material, resulting in persistent non-covalent adsorption without damaging the nanosheet. Bio-conjugation of non-natural moieties with these peptides can incorporate multifunctionality, further extending the applicability of these interfaces. Here, bio-conjugates comprising a graphene-binding peptide with a fatty acid chain of varying length are investigated for their binding affinity and adsorbed structures at the aqueous graphene interface. Through an integration of quartz crystal microbalance and atomic force microscopy data with advanced sampling molecular simulations, variations in the binding of these bio-conjugates is determined. Conjugation at either terminus led to good interfacial contact, and for a given attachment point, the changes in the fatty acid length did not substantially disrupt the conformations of the adsorbed peptide domain. These findings provide a solid foundation for designing multi-functional bio-interfaces for sensing and healthcare.

Ion currents through Kir potassium channels are gated by anionic lipids.

Ion currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook gate of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this gate is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.

Peptide-Driven Exfoliation and Dispersion Mechanisms of Graphene in Aqueous Media.

Peptide-mediated exfoliation and suspension of graphene in aqueous media is a promising strategy for bioapplications such as drug delivery, tissue engineering, and biosensors. A few peptide sequences are known as graphene exfoliators/dispersants in water, but the mechanisms underpinning this process remain underexplored. Here, molecular simulations investigate two key steps: sheet exfoliation and subsequent sheet reunification, in aqueous media. Umbrella sampling simulations predict the energy required to separate a graphene sheet from a graphite stack in both the presence/absence of the graphene-exfoliant peptide, P1. The free-energy barrier for reunification of two P1-coated graphene sheets is similarly calculated. Under sonication, the benefit from the relatively lower free-energy barrier associated with exfoliation in the absence of the peptide is negated by its facile reunification postsonication. In contrast, although P1 slightly increases the energy barrier to exfoliation under sonication, the peptides confer high-energy barriers to sheet reunification, thus ensuring stable aqueous graphene dispersions.

Selective manipulation of peptide orientation on hexagonal boron nitride nanosheets.

The bio-recognition capabilities of materials-specific peptides offer a promising route to obtaining and organizing 2D nanosheet materials in aqueous media. Although significant advances have been made for graphene, little is currently understood regarding how to apply this strategy to hexagonal boron nitride (h-BN) due to a lack of knowledge regarding peptide/h-BN interactions. Here, one of the few peptide sequences known with affinity for h-BN, BP7, is the focus of mutation studies and bio-conjugation. A combination of experimental methods and modeling reveals the importance of Tyrosine in peptide/h-BN interactions. This residue is identified as the key anchoring species, which is then leveraged via bio-conjugation of BP7 to a fatty acid to create new interfacial properties. Specific placement of the fatty acid in the bio-conjugate results in dramatic manipulation of the surface-bound biotic overlayer to generate a highly viscoelastic interface. This viscoelasticity is a consequence of the fatty acid binding, which also down-modulates Tyrosine contact to h-BN, resulting in presentation of the extended peptide to solution. In this orientation, the biomolecule is available for subsequent bioconjugation, providing new pathways to programmable organization and conjugation of h-BN nanosheets in liquid water.

Changing perspectives on how the permeation pathway through potassium channels is regulated.

The primary means by which ion permeation through potassium channels is controlled, and the key to selective intervention in a range of pathophysiological conditions, is the process by which channels switch between non-conducting and conducting states. Conventionally, this has been explained by a steric mechanism in which the pore alternates between two conformations: a 'closed' state in which the conduction pathway is occluded and an 'open' state in which the pathway is sufficiently wide to accommodate fully hydrated ions. Recently, however, 'non-canonical' mechanisms have been proposed for some classes of K+ channels. The purpose of this review is to illuminate structural and dynamic relationships underpinning permeation control in K+ channels, indicating where additional data might resolve some of the remaining issues.

A constricted opening in Kir channels does not impede potassium conduction.

The canonical mechanistic model explaining potassium channel gating is of a conformational change that alternately dilates and constricts a collar-like intracellular entrance to the pore. It is based on the premise that K+ ions maintain a complete hydration shell while passing between the transmembrane cavity and cytosol, which must be accommodated. To put the canonical model to the test, we locked the conformation of a Kir K+ channel to prevent widening of the narrow collar. Unexpectedly, conduction was unimpaired in the locked channels. In parallel, we employed all-atom molecular dynamics to simulate K+ ions moving along the conduction pathway between the lower cavity and cytosol. During simulations, the constriction did not significantly widen. Instead, transient loss of some water molecules facilitated K+ permeation through the collar. The low free energy barrier to partial dehydration in the absence of conformational change indicates Kir channels are not gated by the canonical mechanism.

Thermosensitive Polysaccharide Hydrogel As a Versatile Platform for Prolonged Salmon Calcitonin Release and Calcium Regulation.

The common pathological characteristic of osteoporosis and hypercalcemia is the disorder of calcium homeostasis. Currently, salmon calcitonin (sCT), a clinical regenerative medicine, is an attractive chioice to regulate calcium metabolism for alleviation of osteoporosis and hypercalcemia. Unfortunately, serum sCT is quickly cleared in vivo, leading to its short half-life. Here, we designed a versatile hydrogel, based on salmon calcitonin-oxidized calcium alginate (sCT-OCA) conjugate and hydroxypropyl chitin (HPCH). The release profile showed that sCT could be released from HPCH hydrogels loaded with sCT-OCA conjugate (sCT-OCA-HPCH) for at least 28 days with conformation stability. The cellular test demonstrated that the biocompatible sCT-OCA-HPCH, compared with sCT formulation, had capacity in up-regulating alkaline phosphatase activity (∼63% increase) and promoting calcium to deposit into extracellular matrix (∼42% increase). These results indicated that thermosensitive sCT-OCA-HPCH hydrogel herein is a versatile platform for many applications such as calcium metabolism regulation, osteoporosis treatment, and hypercalcemia therapy.

Molecular evolution of the switch for progesterone and spironolactone from mineralocorticoid receptor agonist to antagonist.

The mineralocorticoid receptor (MR) is highly conserved across vertebrate evolution. In terrestrial vertebrates, the MR mediates sodium homeostasis by aldosterone and also acts as a receptor for cortisol. Although the MR is present in fish, they lack aldosterone. The MR binds progesterone and spironolactone as antagonists in human MR but as agonists in zebrafish MR. We have defined the molecular basis of these divergent responses using MR chimeras between the zebrafish and human MR coupled with reciprocal site-directed mutagenesis and molecular dynamic (MD) simulation based on the crystal structures of the MR ligand-binding domain. Substitution of a leucine by threonine in helix 8 of the ligand-binding domain of the zebrafish MR confers the antagonist response. This leucine is conserved across fish species, whereas threonine (serine in rodents) is conserved in terrestrial vertebrate MR. MD identified an interaction of the leucine in helix 8 with a highly conserved leucine in helix 1 that stabilizes the agonist conformation including the interaction between helices 3 and 5, an interaction which has previously been characterized. This switch in the MR coincides with the evolution of terrestrial vertebrates and of aldosterone synthesis. It was perhaps mandatory if the appearance of aldosterone as a specific mediator of the homeostatic salt retention was to be tolerated. The conformational changes also provide insights into the structural basis of agonism versus antagonism in steroid receptors with potential implications for drug design in this important therapeutic target.

Structural analysis of phosphorylation-associated interactions of human MCC with Scribble PDZ domains.

Scribble is a crucial adaptor protein that plays a pivotal role during establishment and control of cell polarity, impacting many physiological processes ranging from cell migration to immunity and organization of tissue architecture. Scribble harbours a leucine-rich repeat domain and four PDZ domains that mediate most of Scribble's interactions with other proteins. It has become increasingly clear that post-translational modifications substantially impact Scribble-ligand interactions, with phosphorylation being a major modulator of binding to Scribble. To better understand how Scribble PDZ domains direct cell polarity signalling and how phosphorylation impacts this process, we investigated human Scribble interactions with MCC (Mutated in Colorectal Cancer). We systematically evaluated the ability of all four individual Scribble PDZ domains to bind the PDZ-binding motif (PBM) of MCC as well as MCC phosphorylated at the -1 Ser position. We show that Scribble PDZ1 and PDZ3 are the major interactors with MCC, and that modifications to Ser at the -1 position in the MCC PBM only has a minor effect on binding to Scribble PDZ domains. We then examined the structural basis for these observations by determining the crystal structures of Scribble PDZ1 domain bound to both the unphosphorylated MCC PBM as well as phosphorylated MCC. Our structures indicated that phospho-Ser at the -1 position in MCC is not involved in major contacts with Scribble PDZ1, and in conjunction with our affinity measurements suggest that the impact of phosphorylation at the -1 position of MCC must extend beyond a simple modulation of the affinity for Scribble PDZ domains.

Hexapeptide-conjugated calcitonin for targeted therapy of osteoporosis.

The high level of bone metabolism associated with osteopenia and multifocal skeletal fracture remains a challenging clinical problem in osteoporosis patients. Salmon calcitonin (sCT), as a peptide medicine, is able to inhibit osteoclast activity and stimulate osteoblast growth. However, calcitonin receptors (CTRs) are widely distributed in vivo, limiting the specificity and therapeutic effects. Here, we report a bone-seeking hexapeptide (Asp6)-conjugated sCT (sCT-Mal-Asp6) for the targeted treatment of osteoporosis. The sCT-Mal-Asp6 was synthesized via a disulfide re-bridge reaction with high specificity and purity. It was demonstrated that the adsorption of sCT-Mal-Asp6 on hydroxyapatite (HA) was about 5.4 times higher than that of sCT. It was demonstrated a prolonged circulation time and 3-fold higher femur tissue accumulation of sCT-Mal-Asp6. In ovariectomized (OVX) models, sCT-Mal-Asp6 significantly increased the ability to attenuate hypercalcemia and reconstruct the trabecula. Our work provides an efficient approach to targeted and effective osteoporosis treatment.