Intrinsic Flexibility Research Articles

Doped Organic Micro‐Thermoelectric Coolers with Rapid Response Time (Adv. Electron. Mater. 12/2022)

Doped Organic Micro-Thermoelectric Coolers The operation mechanism of doped organic Peltier cooling device is illustrated. Organic semiconductors offer unique opportunities for local cooling devices due to their intrinsic mechanical flexibility, light weight and biocompatibility and could enable novel device concepts for display and healthcare applications. More details can be found in article number 2200629 by Shu-Jen Wang, Heiko Reith, Karl Leo, and co-workers.

Spatially nanoconfined N-type polymer semiconductors for stretchable ultrasensitive X-ray detection

Polymer semiconductors are promising candidates for wearable and skin-like X-ray detectors due to their scalable manufacturing, adjustable molecular structures and intrinsic flexibility. Herein, we fabricated an intrinsically stretchable n-type polymer semiconductor through spatial nanoconfinement effect for ultrasensitive X-ray detectors. The design of high-orientation nanofiber structures and dense interpenetrating polymer networks enhanced the electron-transporting efficiency and stability of the polymer semiconductors. The resultant polymer semiconductors exhibited an ultrahigh sensitivity of 1.52 × 104 μC Gyair−1 cm−2, an ultralow detection limit of 37.7 nGyair s−1 (comparable to the record-low value of perovskite single crystals), and polymer film X-ray imaging was achieved at a low dose rate of 3.65 μGyair s−1 (about 1/12 dose rate of the commercial medical chest X-ray diagnosis). Meanwhile, the hybrid semiconductor films could sustain 100% biaxial stretching strain with minimal degeneracy in photoelectrical performances. These results provide insights into future high-performance, low-cost e-skin photoelectronic detectors and imaging.

Highly conductive and flexible porous carbon nanofibers cloth for high-performance supercapacitor

Porous carbon nanofibers combine the superiorities such as good electrical conductivity, intrinsic and structural flexibility, as well as potential mass production, rendering it an important material for flexible and wearable electronics. Nonetheless, the influence of porous carbon nanofiber's nanostructure on electrochemical performances and mechanical flexibility remains an important open question in the design of high-performance and flexible supercapacitors. To address this matter, herein, we report a systematic study to fabricate the porous carbon nanofibers cloth with both high electrical conductivity and flexibility. Our results indicate that the stress concentration during the bending of porous carbon nanofibers can be efficiently relieved through reducing the size of graphite microcrystals and introducing pores between graphite microcrystals, resulting in good flexibility. Meanwhile, the fabricated porous carbon nanofiber achieves high electrical conductivity (Max. 1600 S/m), which can be directly used as flexible supercapacitor electrode material without introducing a conductive agent and binder. Finally, the flexible supercapacitor electrode based on this porous carbon nanofiber exhibits a high specific capacitance of 184 F/g at a current density of 0.5 A/g. Our win-win strategy provides new insight into the fabrication of flexible porous carbon nanofiber materials, showing great application prospects in the field of flexible supercapacitors.

The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation

Barrier-to-Autointegration Factor (BAF) is a highly conserved DNA binding protein important for genome integrity. Its localization and function are regulated through phosphorylation. Previously reported structures of BAF suggested that it is fully ordered, but our recent NMR analysis revealed that its N-terminal region is flexible in solution and that S4/T3 di-phosphorylation by VRK1 reduces this flexibility. Here, molecular dynamics (MD) simulation was used to unveil the conformational ensembles accessible to the N-terminal region of BAF either unphosphorylated, mono-phosphorylated on S4 or di-phosphorylated on S4/T3 (pBAF) and to reveal the interactions that contribute to define these ensembles. We show that the intrinsic flexibility observed in the N-terminal region of BAF is reduced by S4 phosphorylation and to a larger extent by S4/T3 di-phosphorylation. Thanks to the atomic description offered by MD supported by the NMR study of several BAF mutants, we identified the dynamic network of salt bridge interactions responsible for the conformational restriction involving pS4 and pT3 with residues located in helix α1 and α6. Using MD, we showed that the flexibility in the N-terminal region of BAF depends on the ionic strength and on the pH. We show that the presence of two negative charges of the phosphoryl groups is required for a substantial decrease in flexibility in pBAF. Using MD supported by NMR, we also showed that H7 deprotonation reduces the flexibility in the N-terminal region of BAF. Thus, the conformation of the intrinsically disordered N-terminal region of BAF is highly tunable, likely related to its diverse functions.

Conformational motions and ligand-binding underlying gating and regulation in IP3R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

In-situ cross-linking strategy for stabilizing the LEDC of the solid-electrolyte interphase in lithium-ion batteries

Lithium ion batteries (LIBs) are seriously plagued by the unstability of the lithium ethylene dicarbonate (LEDC), the primary organic reduced product of carbonate-based electrolytes, in solid electrolyte interface (SEI). Herein, we propose an in-situ cross-linking strategy driven by an electrolyte additive of SiCl4 to address this challenge with Si as a representative anode platform for LIBs. The theoretical and experimental results jointly confirmed that during the lithiation process, the SiCl4 additive can spontaneously react with LEDC by in-situ cross-linking to form a stable Si-linked LEDC organic species, which serves as a benign “plasticizer” in the SEI layer to improve its intrinsic flexibility, while the inorganic LiCl formed after the dehalogenation of SiCl4 has an ultralow Li+ diffusion barrier (0.08 eV), which endows the SEI layer with faster ion transport capability. This work provides a new avenue and insight into the design of stable and robust electrode/electrolyte interface of LIBs.

Fight fire with fire: the need for a vaccine based on intrinsic disorder and structural flexibility

The absence of advancement in finding efficient vaccines for several human viruses, such as hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and herpes simplex viruses (HSVs) despite 30, 40, and even 60 years of research, respectively, is unnerving. Among objective reasons for such failure are the highly glycosylated nature of proteins used as primary vaccine targets against these viruses and the presence of neotopes and cryptotopes, as well as high mutation rates of the RNA viruses HCV and HIV-1 and the capability to establish latency by HSVs. However, the lack of success in utilization of the structure-based reverse vaccinology for these viruses is likely to be related to the presence of highly flexible and intrinsically disordered regions in human antibodies (Abs) and the major immunogens of HIV-1, HCV, and HSVs, their surface glycoproteins. This clearly calls for moving from the rational structure-based vaccinology to the unstructural vaccinology based on the utilization of tools designed for the analysis of disordered and flexible proteins, while looking at intrinsically disordered viral antigens and their interactions with intrinsically disordered/flexible Abs.

Analytical Modeling for Flapping Wing Deformation and Kinematics with Beam Flexibility

The intrinsic flexibility of biological flyers’ wings has been well recognized as an efficient way to regulate the performance of their flight through the complex interaction between the surrounding air and the deformation of the wings. However, for vehicles that mimic flying creatures through a flapping protocol, the deformation of the beams on the flapping wings is largely ignored. In this study, based on the elastokinetics method, theoretical models, including a simplified analytical solution, are built to determine the deformation and the kinematics of the flapping wing with beam flexibility. After verifying the models by finite element method simulations and experiments, the flapping kinematics of the wing under various wing conditions is resolved in detail. The analytical theory indicates that the system is fully regulated by two independent parameters. The first one describes the damping effect, which is the product of the driving amplitude and the damping ratio, whereas the second one describes the flexibility of the beam, which is the ratio of the driving angular velocity and the circular natural frequency of the beam. This simple analytical theory neatly captures the kinematics of the wing, which will help to evaluate the performance of the flapping wing with beam flexibility.

Open protocols for docking and MD-based scoring of peptide substrates

The study of protein-peptide interactions is an active research field from an experimental and computational perspective, with the latest presenting challenges to model and simulate the peptides' intrinsic flexibility. Predicting affinities towards protein systems of interest, such as proteases, is crucial to understand the specificity of the interactions and support the discovery of novel substrates. Here we provide a set of computational protocols to run structural and dynamical analysis of protein-peptide complexes from a binding perspective. The protocols are based on state-of-the-art methods, but the code is open and can be customized depending on the user needs. These include a fragment-growing peptide docking protocol to predict bound conformations of flexible peptides, a protocol to extract descriptors from protein-peptide molecular dynamics trajectories, and a workflow to build and test machine learning regression models. As a toy example, we applied the protocols to a serine protease structure with a set of known peptide substrates and random sequences to illustrate the use of the code, which is publicly available at: https://github.com/rochoa85/Protocols-Peptide-Binding

Interaction of lanthanide and actinide with BaHfO3 perovskite: A case study with cerium and uranium

AbstractSpeciation of actinide (An) and lanthanide (Ln) in technologically important ceramics is very important from both fundamental as well as technological aspects. The intrinsic structural flexibility of perovskite containing AO6 and BO12 polyhedra makes them suitable and rich hosts for An and Ln. In this work, emphasis was given to deciphering information such as oxidation state, local dopant site, charge compensating defects, excited state kinetics, and so forth in BaHfO3 (BHO) related to dopant uranium (BHO‐U) and cerium (BHO‐Ce). Several spectroscopic techniques namely, time‐resolved photoluminescence (TRPL), positron annihilation lifetime spectra (PALS), and thermoluminescence (TL) spectroscopy coupled with density functional theory (DFT) were employed to probe the same. Ce and U though are distributed at both Ba and Hf sites, Ce prefers the former, while U prefers the latter site. Uranium on the other hand stabilizes as U6+ in the form of octahedral uranate ion giving green emission. PALS suggested the formation of defects in BHO‐Ce and BHO‐U with oxygen vacancies predominating in the former whereas BHO‐U perovskites are loaded with cation vacancies and vacancy clusters. These cation vacancies are responsible for lower TL output in BHO‐U. TL measurements also suggested cerium doping leads to a higher density of deeper traps in BHO‐Ce compared to uranium doping in BHO‐U which is in concurrence with DFT results and may have implications in designing afterglow phosphors based on perovskite. We believe this work would have a long‐term impact on exploring the potential of perovskite for nuclear waste host and afterglow phosphors applications.

Impact of Loading-Dependent Intrinsic Framework Flexibility on Adsorption in UiO-66

Impact of Loading-Dependent Intrinsic Framework Flexibility on Adsorption in UiO-66

Mechano-Graded Electrodes Mitigate the Mismatch between Mechanical Reliability and Energy Density for Foldable Lithium-Ion Batteries.

Flexible lithium-ion batteries (LIBs) with high energy density are highly desirable for wearable electronics. However, difficult to achieve excellent flexibility and high energy density simultaneously via the current approaches for designing flexible LIBs. To mitigate the mismatch, mechano-graded electrodes with gradient-distributed maximum allowable strain are proposed to endow high-loading-mass slurry-coating electrodes with brilliant intrinsic flexibility without sacrificing energy density. As a proof-of-concept, the up-graded LiNi1/3 Mn1/3 Co1/3 O2 cathodes (≈15mg cm-2 , ≈70µm) and graphite anodes (≈8mg cm-2 , ≈105µm) can tolerate an extremely low bending radius of 400 and 600µm, respectively. Finite element analysis (FEA) reveals that, compared with conventionally homogeneous electrodes, the flexibility of the up-graded electrodes is enhanced by specifically strengthening the upper layer and avoiding crack initiation. Benefiting from this, the foldable pouch cell (required bending radius of ≈600µm) successfully realizes a remarkable figure of merit (FOM, energy density vs bending radius) of 121.3 mWh cm-3 . Moreover, the up-graded-electrodes-based pouch cells can deliver a stable power supply, even under various deformation modes, such as twisting, folding, and knotting. This work proposes new insights for harmonizing the mechanics and electrochemistry of energy storage devices to achieve high energy density under flexible extremes.

Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior.

Selective metal binding is a key requirement not only for the functions of natural metalloproteins but also for the potential applications of artificial metalloproteins in heterogeneous environments such as cells and environmental samples. The selection of transition-metal ions through protein design can, in principle, be achieved through the appropriate choice and the precise positioning of amino acids that comprise the primary metal coordination sphere. However, this task is made difficult by the intrinsic flexibility of proteins and the fact that protein design approaches generally lack the sub-Å precision required for the steric selection of metal ions. We recently introduced a flexible/probabilistic protein design strategy (MASCoT) that allows metal ions to search for optimal coordination geometry within a flexible, yet covalently constrained dimer interface. In an earlier proof-of-principle study, we used MASCoT to generate an artificial metalloprotein dimer, (AB)2, which selectively bound CoII and NiII over CuII (as well as other first-row transition-metal ions) through the imposition of a rigid octahedral coordination geometry, thus countering the Irving-Williams trend. In this study, we set out to redesign (AB)2 to examine the applicability of MASCoT to the selective binding of other metal ions. We report here the design and characterization of a new flexible protein dimer, B2, which displays ZnII selectivity over all other tested metal ions including CuII both in vitro and in cellulo. Selective, anti-Irving-Williams ZnII binding by B2 is achieved through the formation of a unique trinuclear Zn coordination motif in which His and Glu residues are rigidly placed in a tetrahedral geometry. These results highlight the utility of protein flexibility in the design and discovery of selective binding motifs.

The Antibacterial Type VII Secretion System of Bacillus subtilis: Structure and Interactions of the Pseudokinase YukC/EssB.

ABSTRACTType VIIb secretion systems (T7SSb) were recently proposed to mediate different aspects of Firmicutes physiology, including bacterial pathogenicity and competition. However, their architecture and mechanism of action remain largely obscure. Here, we present a detailed analysis of the T7SSb-mediated bacterial competition in Bacillus subtilis, using the effector YxiD as a model for the LXG secreted toxins. By systematically investigating protein-protein interactions, we reveal that the membrane subunit YukC contacts all T7SSb components, including the WXG100 substrate YukE and the LXG effector YxiD. YukC’s crystal structure shows unique features, suggesting an intrinsic flexibility that is required for T7SSb antibacterial activity. Overall, our results shed light on the role and molecular organization of the T7SSb and demonstrate the potential of B. subtilis as a model system for extensive structure-function studies of these secretion machineries.

In vitro characterization of the full-length human dynein-1 cargo adaptor BicD2

Cargo adaptors are crucial in coupling motor proteins with their respective cargos and regulatory proteins. BicD2 is a prominent example within the cargo adaptor family. BicD2 is able to recruit the microtubule motor dynein to RNA, viral particles, and nuclei. The BicD2-mediated interaction between the nucleus and dynein is implicated in mitosis, interkinetic nuclear migration (INM) in radial glial progenitor cells, and neuron precursor migration during embryonic neocortex development. Invitro studies involving full-length cargo adaptors are difficult to perform due to the hydrophobic character, low-expression levels, and intrinsic flexibility of cargo adaptors. Here, we report the recombinant production of full-length human BicD2 and confirm its biochemical activity by interaction studies with RanBP2. We also describe pH-dependent conformational changes of BicD2 using cryoelectron microscopy (cryo-EM), template-free structure predictions, and biophysical tools. Our results will help define the biochemical parameters for the invitro reconstitution of higher-order BicD2 protein complexes.

Measuring the Radius of Gyration and Intrinsic Flexibility of Viral Proteins in Buffer Solution Using Small-Angle X-ray Scattering.

Measuring structural features of proteins dispersed in buffer solution, in contrast to crystal form, is indispensable in understanding morphological characteristics of the biomolecule in a native environment. We report on the structure and apparent viscosity of unfolded α and β variants of SARS-CoV-2 spike proteins dispersed in buffer solutions. The radius of gyration of the β variant is found to be larger than that of the α variant, while the ab initio computation of one of the possible particle-like bodies is consistent with the small-angle X-ray scattering (SAXS) profiles resembling a conformation similar to the three-dimensional structure of the folded state of the corresponding α and β spike variant. However, a smaller radius of gyration with respect to the predicted folded state of 2.4 and 2.7 is observed for both α and β variants, respectively. Our work complements the structural characterization of spike proteins using cryo-electron microscopy techniques. The measurement/analysis discussed here might be useful for quick and cost-effective evaluation of several protein structures, let alone mutated viral proteins, which is useful for drug discovery/development applications.

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2.

The unprecedented performance of Deepmind's Alphafold2 in predicting protein structure in CASP XIV and the creation of a database of structures for multiple proteomes and protein sequence repositories is reshaping structural biology. However, because this database returns a single structure, it brought into question Alphafold's ability to capture the intrinsic conformational flexibility of proteins. Here we present a general approach to drive Alphafold2 to model alternate protein conformations through simple manipulation of the multiple sequence alignment via in silico mutagenesis. The approach is grounded in the hypothesis that the multiple sequence alignment must also encode for protein structural heterogeneity, thus its rational manipulation will enable Alphafold2 to sample alternate conformations. A systematic modeling pipeline is benchmarked against canonical examples of protein conformational flexibility and applied to interrogate the conformational landscape of membrane proteins. This work broadens the applicability of Alphafold2 by generating multiple protein conformations to be tested biologically, biochemically, biophysically, and for use in structure-based drug design.

Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif

Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.

Water Induced Structural Transformations in Flexible Two-Dimensional Layered Conductive Metal–Organic Frameworks

The flexible and ever-changing layered structure of electrically conductive 2D metal–organic frameworks (MOFs) poses a formidable challenge for establishing any structure–application relationships. Here, we employ a combined quantum mechanics and classical molecular dynamics (MD) approach allowing large-scale/long-time simulations of the dynamics of both dry and hydrated systems to investigate the intrinsic flexibility and dynamical motions of layered 2D MOFs and its effect on their physical and chemical properties. The Co3(HHTP)2 and Cu3(HHTP)2 [HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene] MOFs as two representatives of the layered family of MOFs are studied in great details with a focus on their experimentally observed differential framework stabilities in aqueous solutions. Our MD simulations reproduce structural properties of both MOFs as well as a higher tendency of the Co3(HHTP)2 MOF towards water attack and hydrolysis than its Cu3(HHTP)2 counterpart, in agreement with available experimental reports. The results show the presence of two distinctive metastable metal centers with (pseudo)planar vs (pseudo)tetrahedral configurations where the latter are more positively charged than the former and hence more susceptible to water nucleophilic attacks. The accurate ωB97M-v quantum-mechanical calculations show the higher tendency of the open Co2+ sites for coordination to water molecules than the open Cu2+ sites. Our multifaceted strategy paves the way towards simulation of realistic MOF-based materials and their interface with confined water molecules which is especially relevant to designing more robust water stable materials with desired properties and applications.

Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy.

The intrinsically disordered DNA-binding domain of cytidine repressor (CytR-DBD) folds in the presence of target DNA and regulates the expression of multiple genes in E. coli. To explore the conformational rearrangements in the unbound state and the target recognition mechanisms of CytR-DBD, we carried out single-molecule Förster resonance energy transfer (smFRET) measurements. The smFRET data of CytR-DBD in the absence of DNA show one major and one minor population assignable to an expanded unfolded state and a compact folded state, respectively. The population of the folded state increases and decreases upon titration with salt and denaturant, respectively, in an apparent two-state manner. The peak FRET efficiencies of both the unfolded and folded states change continuously with denaturant concentration, demonstrating the intrinsic flexibility of the DNA-binding domain and the deviation from a strict two-state transition. Remarkably, the CytR-DBD exhibits a compact structure when bound to both the specific and nonspecific DNA; however, the peak FRET efficiencies of the two structures are slightly but consistently different. The observed conformational heterogeneity highlights the potential structural changes required for CytR to bind variably spaced operator sequences.