Asymmetric Dimer Research Articles

Allostery in homodimeric SARS-CoV-2 main protease

Many enzymes work as homodimers with two distant catalytic sites, but the reason for this choice is often not clear. For the main protease Mpro of SARS-CoV-2, dimerization is essential for function and plays a regulatory role during the coronaviral replication process. Here, to analyze a possible allosteric mechanism, we use X-ray crystallography, native mass spectrometry, isothermal titration calorimetry, and activity assays to study the interaction of Mpro with three peptide substrates. Crystal structures show how the plasticity of Mpro is exploited to face differences in the sequences of the natural substrates. Importantly, unlike in the free form, the Mpro dimer in complex with these peptides is asymmetric and the structures of the substrates nsp5/6 and nsp14/15 bound to a single subunit show allosteric communications between active sites. We identified arginines 4 and 298 as key elements in the transition from symmetric to asymmetric dimers. Kinetic data allowed the identification of positive cooperativity based on the increase in the processing efficiency (kinetic allostery) and not on the better binding of the substrates (thermodynamic allostery). At the physiological level, this allosteric behavior may be justified by the need to regulate the processing of viral polyproteins in time and space.

Mechanisms of amphibian arrestin 1 self-association and dynamic distribution in retinal photoreceptors

Visual arrestin 1 (Arr1) is an essential protein for termination of the light response in photoreceptors. While mammalian Arr1s form dimers and tetramers at physiological concentrations in vitro, oligomerization in other vertebrates has not been studied. Here we examine self-association of Arr1 from two amphibian species, Xenopus laevis (xArr1), and Ambystoma tigrinum (salArr1). Sedimentation velocity analytical ultracentrifugation showed that xArr1 and salArr1 oligomerization is limited to dimers. The KD for dimer formation was 53 μM for xArr1 and 44 μM for salArr1, similar to the 69 μM KD for bovine Arr1 (bArr1) dimers. Mutations of orthologous amino acids important for mammalian Arr1 oligomerization had no impact on xArr1 dimerization. Crystallography showed that the fold of xArr1 closely resembles that of bArr1 and crystal structures in different space groups revealed two potential xArr1 dimer forms: a symmetrical dimer with a C-domain interface (CC dimer), resembling the bArr1 solution dimer, and an asymmetric dimer with an N-domain/C-domain interface. Mutagenesis of residues predicted to interact in either of these two dimer forms yielded modest reduction in dimer affinity, suggesting that the dimer interfaces compete or are not unique. Indeed, small-angle X-ray scattering and protein painting data were consistent with a symmetric anti-parallel solution dimer (AP dimer) distinct from the assemblies observed by crystallography. Finally, a computational model evaluating xArr1 binding to compartment-specific partners and partitioning based on heterogeneity of available cytoplasmic spaces shows that Arr1 distribution in dark adapted photoreceptors is largely explained by the excluded volume effect together with tuning by oligomerization.

Quasi-bound states in the continuum with stable dual-resonance wavelengths in mid-infrared metasurface for ultrasensitive refractive index sensing and molecular vibrations of strong coupling

In this paper, a dual-resonances mid-infrared all-dielectric metasurface sensor based on asymmetric cross dimer, which is driven by quasi-bound states in the continuum (QBIC), is proposed and investigated. The metasurface sensor maintains the total permittivity constant when the asymmetric parameter is adjusted, thereby ensuring the stability of the QBIC resonance wavelengths, which exhibit Q-factors of 6351 and 13561, respectively. The multiple decompositions and electromagnetic field distributions reveal that the toroidal dipole is the dominant component of the dual-resonance modes. The sensitivities to the refractive index are 3559 nm/RIU and 1146 nm/RIU, with corresponding figures of merit of 4449 RIU−1 and 2453 RIU−1, respectively. Further numerical simulations have demonstrated a strong coupling phenomenon between the QBIC and the molecular vibrations of polymethyl methacrylate (PMMA), resulting in a significant enhancement of the infrared absorption signal. With the 50-nm-thick PMMA layer, the enhancement of molecular signal is 90.614%.

‘Invisible’ Molecular Dynamics Revealed for a Conformationally Chiral π‐Stacked Perylene Bisimide Foldamer

Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis‐PBI 1) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol–1), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re‐fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.

'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer.

Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes 'invisible'. Here we present an asymmetric perylene bisimide dimer (bis-PBI 1) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol-1), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to 'visualize' the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.

Cryo-EM structures of the human band 3 transporter indicate a transport mechanism involving the coupled movement of chloride and bicarbonate ions.

The band 3 transporter is a critical integral membrane protein of the red blood cell (RBC), as it is responsible for catalyzing the exchange of bicarbonate and chloride anions across the plasma membrane. To elucidate the structural mechanism of the band 3 transporter, detergent solubilized human ghost membrane reconstituted in nanodiscs was applied to a cryo-EM holey carbon grid to define its composition. With this approach, we identified and determined structural information of the human band 3 transporter. Here, we present 5 different cryo-EM structures of the transmembrane domain of dimeric band 3, either alone or bound with chloride or bicarbonate. Interestingly, we observed that human band 3 can form both symmetric and asymmetric dimers with a different combination of outward-facing (OF) and inward-facing (IF) states. These structures also allow us to obtain the first model of a human band 3 molecule at the IF conformation. Based on the structural data of these dimers, we propose a model of ion transport that is in favor of the elevator-type mechanism.

Asymmetric dumbbell dimers simultaneously supporting quasi-bound states in continuum and anapole modes for terahertz biosensing

Abstract Multi-resonant metasurfaces are of great significance in the applications of multi-band nanophotonics. Here, we propose a novel metasurface design scheme for simultaneously supporting quasi-bound states in continuum (QBIC) and other resonant modes, in which QBIC resonance is generated by mirror or rotational symmetry breaking in oligomers while other resonant modes can be simultaneously excited by rationally designing the shapes of meta-atoms within oligomers. As an example, the simultaneous excitation of QBIC and anapole modes are demonstrated in a dimer metasurface composed of asymmetric dumbbell-shaped apertures. Based on the far-field multipole decomposition and near-field electromagnetic field distributions, the origin mechanisms of QBIC and anapole mode are elucidated. The symmetry breaking of dumbbell-shaped dimer results in QBIC. Within a certain asymmetric variation range, the contributions of toroidal dipole moment and electric dipole moment with approximately equal magnitudes remain dominant, which allows the anapole mode to always present. The effectiveness of the proposed design scheme is further confirmed by the experimental results identical with the evolutions of numerical simulation. In terahertz biosensing experiments, the anapole mode exhibits a higher sensitivity of 271.3 GHz (nmol/μl)−1, whereas the QBIC can achieve a lower detection limit of 0.015 nmol/μl and expands the detection range by almost an order of magnitude. Our findings are beneficial to designing multi-resonant metasurfaces with different resonance modes and promote the corresponding applications in the fields of biosensing, lasers, filtering, and nonlinearity.

Isoxerophilusins A and B, Two Novel Polycyclic Asymmetric Diterpene Dimers from Isodon xerophilus: Structural Elucidation, Modification, and Inhibitory Activities against α-Glucosidase.

Isoxerophilusins A (1) and B (2), two unprecedented diterpene heterodimers biogenetically from ent-atisanes and abietanes, were isolated from the rhizomes of Isodon xerophilus. Their structures were determined by extensive spectroscopic analysis and single-crystal X-ray diffraction. Selective esterification of 1 generated 11 new derivatives. All derivatives showed excellent α-glucosidase inhibitory activity in comparison to acarbose. Compounds 12 and 13 demonstrated significant inhibition against α-glucosidase with IC50 values of 4.92 and 3.83 μM, respectively.

A Series of Cyclopentadienyl Lanthanum Complexes with Metalloid Germanium Clusters.

A series of cyclopentadienyllanthanum complexes with the disilylated metalloid germanium cluster [Ge9(Hyp)2]2- [Hyp = Si(SiMe3)3] has been prepared and fully characterized. The synthetic procedure is based on the salt metathesis reaction of two different cyclopentadienyllanthanum diiodides CpLaI2 (Cp: Cp*, pentamethylcyclopentadienyl; Cpttt, 1,2,4-tri-tert-butylcyclopentadienyl) with K2[Ge9(Hyp)2] in tetrahydrofuran (THF) with a subsequent extraction with n-hexane. The composition of the obtained compounds and the mode of coordination of the germanium cluster to the rare-earth metal are strongly influenced by the steric demand of the cyclopentadienyl ligands and the crystallization conditions. The centrosymmetric dimeric compounds with the common formula [CpLa(solv)(η2,3-Ge9(Hyp)2)]2 [1, Cp = Cp*, solv-THF; 2, Cp = Cpttt, solv-NCCH2C(Me)NSiMe3] have been isolated by the slow evaporation of a n-hexane solution, while a mononuclear complex [CptttLa(THF)2(η3-Ge9(Hyp)2)] (4) was found by crystallization from THF. The repeated recrystallization of 1 from n-hexane afforded the asymmetric dimer [Cp*La(THF)(η2,3-Ge9(Hyp)2)][Cp*La(η2,3-Ge9(Hyp)2)] (3) with only one coordinated THF molecule.

Toroidal dipole bound states in the continuum in asymmetric dimer metasurfaces

Structural symmetry plays a pivotal role in the emergence of symmetry-protected bound states in the continuum (BICs), often observed at the Γ-point within the first Brillouin zone. However, structural symmetry is not an absolute requirement for the formation of BICs at the Γ-point. In this work, we demonstrate that all-dielectric metasurfaces and photonic crystal slabs, made of dimer nanostructures with different sizes and shapes, can sustain BICs at the Γ-point. We show that the nature of these BICs is well preserved, irrespective of the size mismatch/difference, as long as the center-to-center distance between two nanodisks is equal to half of the lattice constants of a superunit cell. The BICs are transformed into quasi-BICs (QBICs) with finite quality (Q) factors by varying the interspacing of dimer nanodisks. Multipole decomposition indicates that this BIC is primarily governed by a toroidal dipole, with a secondary contribution from a magnetic dipole and magnetic quadrupole. Furthermore, we establish that such a BIC is robust against the shape of nanodisks. Notably, we observe that the Q-factor of QBICs for right nanodisks displaced along the y-axis is three orders of magnitude higher than those along the x-axis, suggesting an effective approach to realizing ultrahigh-Q resonances. Finally, we present an experimental demonstration of such a BIC by fabricating silicon dimer metasurfaces and photonic crystal slabs with dimer nanoholes. The trend of measured Q-factors and resonant wavelengths of QBICs shows good agreement with theoretical predictions. The maximum Q-factor is up to 22 633. These results not only advance our understanding of BICs within compound metasurfaces but also hold great promise in enhancing light–matter interactions.

Rational Design of Cyanine-Based Fluorogenic Dimers to Reduce Nonspecific Interactions with Albumin and Lipid Bilayers: Application to Highly Sensitive Imaging of GPCRs in Living Cells.

Fluorogenic dimers with polarity-sensitive folding are powerful probes for live-cell bioimaging. They switch on their fluorescence only after interacting with their targets, thus leading to a high signal-to-noise ratio in wash-free bioimaging. We previously reported the first near-infrared fluorogenic dimers derived from cyanine 5.5 dyes for the optical detection of G protein-coupled receptors. Owing to their hydrophobic character, these dimers are prone to form nonspecific interactions with proteins such as albumin and with the lipid bilayer of the cell membrane resulting in a residual background fluorescence in complex biological media. Herein, we report the rational design of new fluorogenic dimers derived from cyanine 5. By modulating the chemical structure of the cyanine units, we discovered that the two asymmetric cyanine 5.25 dyes were able to form intramolecular H-aggregates and self-quenched in aqueous media. Moreover, the resulting original dimeric probes enabled a significant reduction of the nonspecific interactions with bovine serum albumin and lipid bilayers compared with the first generation of cyanine 5.5 dimers. Finally, the optimized asymmetric fluorogenic dimer was grafted to carbetocin for the specific imaging of the oxytocin receptor under no-wash conditions directly in cell culture media, notably improving the signal-to-background ratio compared with the previous generation of cyanine 5.5 dimers.

Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI

Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.

Symmetry-breaking-induced off-resonance second-harmonic generation enhancement in asymmetric plasmonic nanoparticle dimers

Abstract The linear and nonlinear optical properties of metallic nanoparticles have attracted considerable experimental and theoretical research interest. To date, most researchers have focused primarily on exploiting their plasmon excitation enhanced near-field and far-field responses and related applications in sensing, imaging, energy harvesting, conversion, and storage. Among numerous plasmonic structures, nanoparticle dimers, being a structurally simple and easy-to-prepare system, hold significant importance in the field of nanoplasmonics. In highly symmetric plasmonic nanostructures, although the odd-order optical nonlinearity of the near-surface region will be improved because of the enhanced near-fields, even-order nonlinear processes such as second-harmonic generation (SHG) will still be quenched and thus optically forbidden. Under this premise, it is imperative to introduce structural symmetry breaking to realize plasmon-enhanced even-order optical nonlinearity. Here, we fabricate a series of nanoparticle dimers each composed of two gold nanospheres with different diameters and subsequently investigate their structural asymmetry dependent linear and nonlinear optical properties. We find that the SHG intensities of gold nanosphere dimers are significantly enhanced by structural asymmetry under off-resonance excitation while the plasmonic near-field enhancement mainly affects SHG under on-resonance excitation. Our results reveal that symmetry breaking will play an indispensable role when designing novel coupled plasmonic nanostructures with enhanced nonlinear optical properties.

Cryo-EM structures of Thogoto virus polymerase reveal unique RNA transcription and replication mechanisms among orthomyxoviruses

Influenza viruses and thogotoviruses account for most recognized orthomyxoviruses. Thogotoviruses, exemplified by Thogoto virus (THOV), are capable of infecting humans using ticks as vectors. THOV transcribes mRNA without the extraneous 5′ end sequences derived from cap-snatching in influenza virus mRNA. Here, we report cryo-EM structures to characterize THOV polymerase RNA synthesis initiation and elongation. The structures demonstrate that THOV RNA transcription and replication are able to start with short dinucleotide primers and that the polymerase cap-snatching machinery is likely non-functional. Triggered by RNA synthesis, asymmetric THOV polymerase dimers can form without the involvement of host factors. We confirm that, distinctive from influenza viruses, THOV-polymerase RNA synthesis is weakly dependent of the host factors ANP32A/B/E in human cells. This study demonstrates varied mechanisms in RNA synthesis and host factor utilization among orthomyxoviruses, providing insights into the mechanisms behind thogotoviruses’ broad-infectivity range.

Tunable Plasmonic Properties of Spatially Overlapping Asymmetric Nanoparticle Dimers

Tunable Plasmonic Properties of Spatially Overlapping Asymmetric Nanoparticle Dimers

Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation

Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer—the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA.

Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model.

Epidermal growth factor receptor (EGFR) activation is accompanied by dimerization. During the activation of the intracellular kinase domain, two EGFR kinases form an asymmetric dimer, and one side of the dimer (receiver) is activated. Using the string method and Markov state model (MSM), we performed a computational analysis of the structural changes in the activation of the EGFR dimer in this study. The string method reveals the minimum free-energy pathway (MFEP) from the inactive to active structure. The MSM was constructed from numerous trajectories of molecular dynamics simulations around the MFEP, which revealed the free-energy map of structural changes. In the activation of the receiver kinase, the unfolding of the activation loop (A-loop) is followed by the rearrangement of the C-helix, as observed in other kinases. However, unlike other kinases, the free-energy map of EGFR at the asymmetric dimer showed that the active state yielded the highest stability and revealed how interactions at the dimer interface induced receiver activation. As the H-helix of the activator approaches the C-helix of the receiver during activation, the A-loop unfolds. Subsequently, L782 of the receiver enters the pocket between the G- and H-helices of the activator, leading to a rearrangement of the hydrophobic residues around L782 of the receiver, which constitutes a structural rearrangement of the C-helix of the receiver from an outward to an inner position. The MSM analysis revealed long-time scale trajectories via kinetic Monte Carlo.

Reliable detection of malachite green by self-assembled SERS substrates based on gold–silicon heterogeneous nano pineapple structures

Morphology regulation of heterodimer nanoparticles and the use of their asymmetric features for further practical applications are crucial because of the rich optical properties and various combinations of heterodimers. This work used silicon to asymmetrically wrap half of a gold sphere and grew gold branches on the bare gold surface to form heterogeneous nano pineapples (NPPs) which can effectively improve Surface-enhanced Raman scattering (SERS) properties through chemical enhancement and lightning-rod effect respectively. The asymmetric structures of NPPs enabled them to self-assemble into the monolayer membrane with consistent branch orientation. The prepared substrate had high homogeneity and better SERS ability than disorganized substrates, and achieved reliable detection of malachite green (MG) in clams with a detection limit of 7.8 × 10−11 M. This work provided a guide to further revise the morphology of heterodimers and a new idea for the use of asymmetric dimers for practically photochemical and biomedical sensing.

Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB.

In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to fine-tune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.

A Janus carbaporphyrin pseudo-dimer

Carbaporphyrin dimers, investigated for their distinctive electronic structures and exceptional properties, have predominantly consisted of systems containing identical subunits. This study addresses the associated knowledge gap by focusing on asymmetric carbaporphyrin dimers with Janus-like characteristics. The synthesis of a Janus-type carbaporphyrin pseudo-dimer 5 is presented. It displays antiaromatic characteristics on the fused side and nonaromatic behavior on the unfused side. A newly synthesized tetraphenylene (TPE) linked bis-dibenzihomoporphyrin 8 and a previously reported dibenzo[g,p]chrysene (DBC) linked bis-dicarbacorrole 9 were prepared as controls. Comprehensive analyses, including 1H NMR spectral studies, single crystal X-ray diffraction analyses, and DFT calculations, validate the mixed character of 5. A further feature of the Janus pseudo-dimer 5 is that it may be transformed into a heterometallic complex, with one side coordinating a Cu(III) center and the other stabilizing a BODIPY complex. This disparate regiochemical reactivity underscores the potential of carbaporphyrin dimers as versatile frameworks, with electronic features and site-specific coordination chemistry controlled through asymmetry. These findings position carbaporphyrin dimers as promising candidates for advances in electronic structure studies, coordination chemistry, materials science, and beyond.