Modulating the folding and binding of peptides using a stimuli-responsive molecular tweezer

This study presents the development of a β-hairpin (tryptophan zipper, Trpzip)-based molecular tweezer (MT) that can control the folding and binding of α-helical peptides. When an α-helix isolated from the p53 protein was conjugated with Trpzip in an optimized macrocyclic structure, the folded β-hairpin stabilized the helix conformation through the side chain-to-side chain stapling strategy, which notably enhanced target (hDM2) affinity of the peptide. On the other hand, the helicity and binding affinity were significantly reduced when the hairpin was unfolded by a redox stimulus. This stimulus-responsive property was translated into the effective capture and release of model multivalent biomaterials, hDM2-gold nanoparticle conjugates. Since numerous protein interactions are mediated by α-helical peptides, these results suggest that the β-hairpin-based MT holds great potential to be utilized in various biomedical applications, such as protein interaction inhibition and cancer biomarker (e.g., circulating tumor cells and exosomes) detection.

Synchrotron X-ray study of intrinsically disordered and polyampholytic Tau 4RS and 4RL under controlled ionic strength

Aggregated and hyperphosphorylated Tau is one of the pathological hallmarks of Alzheimer's disease. Tau is a polyampholytic and intrinsically disordered protein (IDP). In this paper, we present for the first time experimental results on the ionic strength dependence of the radius of gyration (Rg) of human Tau 4RS and 4RL isoforms. Synchrotron X-ray scattering revealed that 4RS Rg is regulated from 65.4 to 58.5 Å and 4RL Rg is regulated from 70.9 to 57.9 Å by varying ionic strength from 0.01 to 0.592 M. The Rg of 4RL Tau is larger than 4RS at lower ionic strength. This result provides an insight into the ion-responsive nature of intrinsically disordered and polyampholytic Tau, and can be implicated to the further study of Tau-Tau and Tau-tubulin intermolecular structure in ionic environments.

USP35 dimer prevents its degradation by E3 ligase CHIP through auto-deubiquitinating activity

Recently, a number of reports on the importance of USP35 in cancer have been published. However, very little is known about the exact mechanism by which USP35 activity is regulated. Here, we show the possible regulation of USP35 activity and the structural specificity affecting its function by analyzing various fragments of USP35. Interestingly, the catalytic domain of USP35 alone does not exhibit deubiquitinating activity; in contrast, the C-terminal domain and insertion region in the catalytic domain is required for full USP35 activity. Additionally, through its C-terminal domain, USP35 forms a homodimer that prevents USP35 degradation. CHIP bound to HSP90 interacts with and ubiquitinates USP35. However, when fully functional USP35 undergoes auto-deubiquitination, which attenuates CHIP-mediated ubiquitination. Finally, USP35 dimer is required for deubiquitination of the substrate Aurora B and regulation of faithful mitotic progression. The properties of USP35 identified in this study are a unique homodimer structure, regulation of deubiquitinating activity through this, and utilization of a novel E3 ligase involved in USP35 auto-deubiquitination, which adds another complexity to the regulation of deubiquitinating enzymes.

Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex

Cupriavidus necator H16 is a gram-negative chemolithoautotrophic bacterium that has been extensively studied for biosynthesis and biodegradation of polyhydroxyalkanoate (PHA) plastics. To improve our understanding of fatty acid metabolism for PHA production, we determined the crystal structure of multi-functional enoyl-CoA hydratase from Cupriavidus necator H16 (CnFadB). The predicted model of CnFadB created by AlphaFold was used to solve the phase problem during determination of the crystal structure of the protein. The CnFadB structure consists of two distinctive domains, an N-terminal enol-CoA hydratase (ECH) domain and a C-terminal 3-hydroxyacyl-CoA dehydrogenase (HAD) domain, and the substrate- and cofactor-binding modes of these two functional domains were identified. Unlike other known FadB enzymes that exist as dimers complexed with FadA, CnFadB functions as a monomer without forming a complex with CnFadA. Small angle X-ray scattering (SAXS) measurement further proved that CnFadB exists as a monomer in solution. The non-sequential action of FadA and FadB in C. necator appears to affect β-oxidation and PHA synthesis/degradation.

Structural features of a minimal intact methyltransferase of a type I restriction-modification system

Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M₂S₁ MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S_1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M₁S_1/2)₂ structure reveals a symmetric (S_1/2)₂ assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M₁S_1/2 MTase dimer indicates a particular state resembling the structure of M₂S₁ MTases.

Structural transition of reverse cylindrical micelles to reverse vesicles by mixtures of lecithin and inorganic salts

HYPOTHESIS

The transformation from reverse micelles to reverse vesicles is influenced by electrostatic interactions between lecithin headgroups and inorganic salts. The electrostatic interactions are expected to influence molecular geometry of lecithin, resulting in a reduction in critical packing parameter (p). Hence, it should be possible to drive structural transitions of reverse self-assembled structures by addition of inorganic salts to lecithin solutions.

EXPERIMENTS

Structural transitions of reverse micelles and reverse vesicles were formulated including lecithin and inorganic salts as a function of concentration in cyclohexane. A systematic study was performed using inorganic salts with the different valences of the cations such as Li⁺, Ca²⁺, and La³⁺. To probe the nanodomain structures from the lecithin/salt mixtures, small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) were used.

FINDINGS

Adding salts to lecithin solutions induced the systematic transformation of reverse self-assembled structures from reverse spherical micelles to reverse cylindrical micelles and finally to reverse vesicles. The transformation was also correlated with interactions between lecithin headgroups and salts, that is, Li⁺ < Ca²⁺ < La³⁺. In addition, a water-soluble dye such as rhodamine B (RB) can be readily encapsulated into reverse micelles and vesicles, indicating that they are potentially useful for controlled solute delivery.

Newly Found Digital Memory Characteristics of Pyrrolidone- and Succinimide-Based Polymers

This study reports for the first time the excellent nonvolatile and volatile digital memory characteristics of polymers bearing 2-pyrrolidone and succinimide moieties. A series of new polymers is synthesized from poly(ethylene-alt-maleic anhydride) and four alcohol derivatives with and without 2-pyrrolidone and succinimide moieties. All polymers, including polyvinylpyrrolidone, are found to be thermally stable up to 195 °C or higher, and characterized regarding their molecular orbital energy levels, bandgap, and resistive digital memory behaviors. Excitingly, the polymers bearing either 2-pyrrolidone or succinimide moiety demonstrate p-type digital memory behaviors with high ON/OFF current ratios and long reliabilities. Nonvolatile digital memory performance is achieved over the film thickness range of 10-80 nm, whereas volatile digital memory is demonstrated over a much narrower range of film thickness. All digital memory performances can be originated from the 2-pyrrolidone and succinimide moieties possessing high affinity and stabilization power to charges via charge traps and transformations based on a hopping conduction process. Hence, these new polymers are suitable for the production of high-performance p-type nonvolatile and volatile digital memory devices. Moreover, 2-pyrrolidone and succinimide can be used as new and economical electroactive building blocks for the development of advanced digital memory materials.

Molecular Analysis of the Interaction between Human PTPN21 and the Oncoprotein E7 from Human Papillomavirus Genotype 18

Human papillomaviruses (HPVs) cause cellular hyperproliferation-associated abnormalities including cervical cancer. The HPV genome encodes two major viral oncoproteins, E6 and E7, which recruit various host proteins by direct interaction for proteasomal degradation. Recently, we reported the structure of HPV18 E7 conserved region 3 (CR3) bound to the protein tyrosine phosphatase (PTP) domain of PTPN14, a well-defined tumor suppressor, and found that this intermolecular interaction plays a key role in E7-driven transformation and tumorigenesis. In this study, we carried out a molecular analysis of the interaction between CR3 of HPV18 E7 and the PTP domain of PTPN21, a PTP protein that shares high sequence homology with PTPN14 but is putatively oncogenic rather than tumor-suppressive. Through the combined use of biochemical tools, we verified that HPV18 E7 and PTPN21 form a 2:2 complex, with a dissociation constant of 5 nM and a nearly identical binding manner with the HPV18 E7 and PTPN14 complex. Nevertheless, despite the structural similarities, the biological consequences of the E7 interaction were found to differ between the two PTP proteins. Unlike PTPN14, PTPN21 did not appear to be subjected to proteasomal degradation in HPV18-positive HeLa cervical cancer cells. Moreover, knockdown of PTPN21 led to retardation of the migration/invasion of HeLa cells and HPV18 E7-expressing HaCaT keratinocytes, which reflects its protumor activity. In conclusion, the associations of the viral oncoprotein E7 with PTPN14 and PTPN21 are similar at the molecular level but play different physiological roles.

Seventeen-Armed Star Polystyrenes in Various Molecular Weights: Structural Details and Chain Characteristics

Star-shaped polymers are very attractive because of their potential application ability in various technological areas due to their unique molecular topology. Thus, information on the molecular structure and chain characteristics of star polymers is essential for gaining insights into their properties and finding better applications. In this study, we report molecular structure details and chain characteristics of 17-armed polystyrenes in various molecular weights: 17-Arm(2k)-PS, 17-Arm(6k)-PS, 17-Arm(10k)-PS, and 17-Arm(20k)-PS. Quantitative X-ray scattering analysis using synchrotron radiation sources was conducted for this series of star polymers in two different solvents (cyclohexane and tetrahydrofuran), providing a comprehensive set of three-dimensional structure parameters, including radial density profiles and chain characteristics. Some of the structural parameters were crosschecked by qualitative scattering analysis and dynamic light scattering. They all were found to have ellipsoidal shapes consisting of a core and a fuzzy shell; such ellipse nature is originated from the dendritic core. In particular, the fraction of the fuzzy shell part enabling to store desired chemicals or agents was confirmed to be exceptionally high in cyclohexane, ranging from 74 to 81%; higher-molecular-weight star polymer gives a larger fraction of the fuzzy shell. The largest fraction (81%) of the fuzzy shell was significantly reduced to 52% in tetrahydrofuran; in contrast, the lowest fraction (19%) of core was increased to 48%. These selective shell contraction and core expansion can be useful as a key mechanism in various applications. Overall, the 17-armed polystyrenes of this study are suitable for applications in various technological fields including smart deliveries of drugs, genes, biomedical imaging agents, and other desired chemicals.

Mechanism for Transition of Reverse Cylindrical Micelles to Spherical Micelles Induced by Diverse Alcohols

Herein, the effects of various alcohols on lecithin/CaCl₂ organogels are investigated. Mixtures of lecithin and CaCl₂ form reverse cylindrical micelles, resulting in optically transparent organogels. The addition of various alcohols to a mixture of lecithin and CaCl₂ induces a decrease in viscosity through which reverse cylindrical micelles are transformed into spherical micelles (or short cylindrical micelles). Long-hydrocarbon-chain alcohols decrease the viscosity of lecithin/CaCl₂ mixtures more efficiently. Hydrogen bonding and hydrocarbon chain interactions between lecithin and alcohol play important roles in the morphological transition. More importantly, isothermal titration calorimetry was conducted to obtain thermodynamic variables such as the enthalpy, equilibrium constant, Gibbs free energy, entropy, and stoichiometry of the associated molecules observed in the transition. It was found that the transition is an entropically driven process, in which the endothermic and exothermic behaviors were observed depending on the hydrocarbon chain length in the alcohol. In addition, the enthalpy for the association of the alcohol with lecithin showed a linear relationship depending on the hydrocarbon chain length, in which the magnitude of hydrogen bonding and hydrocarbon chain interactions was obtained quantitatively. To the best of our knowledge, this is the first study reporting the thermodynamic properties of the morphological transition observed in a reverse self-assembly process.

Structural insights into the regulation of SigB activity by RsbV and RsbW

Bacillus subtilis SigB is an alternative sigma factor that initiates the transcription of stress-responsive genes. The anti-sigma factor RsbW tightly binds SigB to suppress its activity under normal growth conditions and releases it when nonphosphorylated RsbV binds to RsbW in response to stress signals. To understand the regulation of SigB activity by RsbV and RsbW based on structural features, crystal structures and a small-angle X-ray scattering (SAXS) envelope structure of the RsbV-RsbW complex were determined. The crystal structures showed that RsbV and RsbW form a heterotetramer in a similar manner to a SpoIIAA-SpoIIAB tetramer. Multi-angle light scattering and SAXS revealed that the RsbV-RsbW complex is an octamer in solution. Superimposition of the crystal structure on the SAXS envelope structure showed that the unique dimeric interface of RsbW mediates the formation of an RsbV-RsbW octamer and does not prevent RsbV and SigB from binding to RsbW. These results provide structural insights into the molecular assembly of the RsbV-RsbW complex and the regulation of SigB activity.

Structural and Molecular Basis for Katanin-Mediated Severing of Glutamylated Microtubules

Katanin was the first microtubule (MT)-severing enzyme discovered, but how katanin executes MT severing remains poorly understood. Here, we report X-ray crystal structures of the apo and ATPγS-bound states of the catalytic AAA domain of human katanin p60 at 3.0 and 2.9 Å resolution, respectively. Comparison of the two structures reveals conformational changes induced by ATP binding and how such changes ensure hexamer stability. Moreover, we uncover structural details of pore loops (PLs) and show that Arg283, a residue unique to katanin among MT-severing enzymes, protrudes from PL1 and lines the entry of the catalytic pore. Functional studies suggest that PL1 and Arg283 play essential roles in the recognition and remodeling of the glutamylated, C-terminal tubulin tail and regulation of axon growth. In addition, domain-swapping experiments in katanin and spastin suggest that the non-homologous N-terminal region, which contains the MT-interacting and trafficking domain and a linker, confers specificity to the severing process.

Quantitative Structural Analysis of Polystyrene Nanoparticles Using Synchrotron X-Ray Scattering and Dynamic Light Scattering

A series of polystyrene nanoparticles (PS-1, PS-2, PS-3, and PS-4) in aqueous solutions were investigated in terms of morphological structure, size, and size distribution. Synchrotron small-angle X-ray scattering analysis (SAXS) was carried out, providing morphology details, size and size distribution on the particles. PS-1, PS-2, and PS-3 were confirmed to behave two-phase (core and shell) spherical shapes, whereas PS-4 exhibited a single-phase spherical shape. They all revealed very narrow unimodal size distributions. The structural parameter details including radial density profile were determined. In addition, the presence of surfactant molecules and their assemblies were detected for all particle solutions, which could originate from their surfactant-assisted emulsion polymerizations. In addition, dynamic light scattering (DLS) analysis was performed, finding only meaningful hydrodynamic size and intensity-weighted mean size information on the individual PS solutions because of the particles' spherical nature. In contrast, the size distributions were extracted unrealistically too broad, and the volume- and number-weighted mean sizes were too small, therefore inappropriate to describe the particle systems. Furthermore, the DLS analysis could not detect completely the surfactant and their assemblies present in the particle solutions. Overall, the quantitative SAXS analysis confirmed that the individual PS particle systems were successfully prepared with spherical shape in a very narrow unimodal size distribution.

Structural insight into bi-functional malonyl-CoA reductase

The bi-functional malonyl-CoA reductase is a key enzyme of the 3-hydroxypropionate bi-cycle for bacterial CO₂ fixation, catalysing the reduction of malonyl-CoA to malonate semialdehyde and further reduction to 3-hydroxypropionate. Here, we report the crystal structure and the full-length architecture of malonyl-CoA reductase from Porphyrobacter dokdonensis. The malonyl-CoA reductase monomer of 1230 amino acids consists of four tandemly arranged short-chain dehydrogenases/reductases, with two catalytic and two non-catalytic short-chain dehydrogenases/reductases, and forms a homodimer through paring contact of two malonyl-CoA reductase monomers. The complex structures with its cofactors and substrates revealed that the malonyl-CoA substrate site is formed by the cooperation of two short-chain dehydrogenases/reductases and one novel extra domain, while only one catalytic short-chain dehydrogenase/reductase contributes to the formation of the malonic semialdehyde-binding site. The phylogenetic and structural analyses also suggest that the bacterial bi-functional malonyl-CoA has a structural origin that is completely different from the archaeal mono-functional malonyl-CoA and malonic semialdehyde reductase, and thereby constitute an efficient enzyme.

Chemically Denatured Structures of Porcine Pepsin using Small-Angle X-ray Scattering

Porcine pepsin is a gastric aspartic proteinase that reportedly plays a pivotal role in the digestive process of many vertebrates. We have investigated the three-dimensional (3D) structure and conformational transition of porcine pepsin in solution over a wide range of denaturant urea concentrations (0–10 M) using Raman spectroscopy and small-angle X-ray scattering. Furthermore, 3D GASBOR ab initio structural models, which provide an adequate conformational description of pepsin under varying denatured conditions, were successfully constructed. It was shown that pepsin molecules retain native conformation at 0–5 M urea, undergo partial denaturation at 6 M urea, and display a strongly unfolded conformation at 7–10 M urea. According to the resulting GASBOR solution models, we identified an intermediate pepsin conformation that was dominant during the early stage of denaturation. We believe that the structural evidence presented here provides useful insights into the relationship between enzymatic activity and conformation of porcine pepsin at different states of denaturation.

Characterization of a Dimeric Arginase From Zymomonas mobilis ZM4

Many organisms have genes to protect themselves from toxic conditions such as high ethanol and/or ammonia concentrations. When a high ethanol condition is induced to Zymomonas mobilis ZM4, a representative ethanologenic organism, this bacterium overexpresses several genes to overcome this ethanol stress. Among them, we characterized a gene product annotated as an arginase (zmARG) from Z. mobilis ZM4. Even though all of the arginase-determining sequence motifs are not strictly conserved in zmARG, this enzyme converts L-arginine to urea and L-ornithine in the presence of a divalent manganese ion. The revealed high-resolution crystal structure of zmARG shows that it has a typical globular α/β arginase fold with a protruded C-terminal helix. Two zinc ions reside in the active site, where one metal ion is penta-coordinated and the other has six ligands, discerning this zmARG from the reported arginases with two hexa-liganded metal ions. zmARG forms a dimeric structure in solution as well as in the crystalline state. The dimeric assembly of zmARG is formed mainly by interaction formed between the C-terminal α-helix of one molecule and the α/β hydrolase fold of another molecule. The presented findings demonstrate the first reported dimeric arginase formed by the C-terminal tail and has two metal ions coordinated by different number of ligands.

Symmetric Assembly of a Decameric Subcomplex in Human Multi-tRNA Synthetase Complex Via Interactions between Glutathione Transferase-Homology Domains and Aspartyl-tRNA Synthetase

Aminoacyl-tRNA synthetases (AARSs) ligate amino acids to their cognate tRNAs during protein synthesis. In humans, eight AARSs and three non-enzymatic AARS-interacting multifunctional proteins (AIMP1-3), which are involved in various biological processes, form a multi-tRNA synthetase complex (MSC). Elucidation of the structures and multiple functions of individual AARSs and AIMPs has aided current understanding of the structural arrangement of MSC components and their assembly processes. Here, we report the crystal structure of a complex comprising a motif from aspartyl-tRNA synthetase (DRS) and the glutathione transferase (GST)-homology domains of methionyl-tRNA synthetase (MRS), glutamyl-prolyl-tRNA synthetase (EPRS), AIMP2, and AIMP3. In the crystal structure, the four GST domains are assembled in the order of MRS-AIMP3-EPRS-AIMP2, and the GST domain of AIMP2 binds DRS through the β-sheet in the GST domain. The C-terminus of AIMP3 enhances the binding of DRS to the tetrameric GST complex. A DRS dimer and two GST tetramers binding to the dimer with 2-fold symmetry complete a decameric complex. The formation of this complex enhances the stability of DRS and enables it to retain its reaction intermediate, aspartyl adenylate. Since the catalytic domains of MRS and EPRS are connected to the decameric complex through their flexible linker peptides, and lysyl-tRNA synthetase and AIMP1 are also linked to the complex via the N-terminal region of AIMP2, the DRS-GST tetramer complex functions as a frame in the MSC.

Micelle-Assisted Formation of Nanoparticle Superlattices and Thermally Reversible Symmetry Transitions

Nanoparticle superlattices (NPSLs) are of great interest as materials with designed emerging properties depending on the lattice symmetry as well as composition. The symmetry transition of NPSLs depending on environmental conditions can be an excellent ground for making new stimuli-responsive functional materials. Here, we report a spherical micelle-assisted method to form exceptionally ordered NPSLs which are inherently sensitive to environmental conditions. Upon mixing functionalized gold nanoparticles (AuNPs) with a nonionic surfactant spherical micellar solution, NPSLs of different symmetries such as NaZn₁₃, MgZn₂, and AlB₂-type are formed depending on the size ratio between micelles and functionalized AuNPs and composition. The NPSLs formed by the spherical micelle-assisted method show thermally reversible order-order (NaZn₁₃-AlB₂) and order-disorder (MgZn₂-isotropic) symmetry transitions, which are consistent with the Gibbs free energy calculations for binary hard-sphere model. This approach may open up new possibilities for NPSLs as stimuli-responsive functional materials.

Structural and Physiological Exploration of Salmonella Typhi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence

YfdX is a prokaryotic protein encoded by several pathogenic bacteria including Salmonella enterica serovar Typhi, which causes one of the most fatal infectious diseases, typhoid fever. YfdX is a product of the yfdXWUVE operon and is known to be under the control of EvgA, a regulator protein controlling the expression of several proteins involved in response to environmental stress, in Escherichia coli. Nevertheless, unlike other proteins encoded by the same operon, the structural and physiological aspects of YfdX have been poorly characterized. Here, we identified a previously unknown pH-dependent stoichiometric conversion of S. Typhi YfdX between dimeric and tetrameric states; this conversion was further analyzed via determining its structure by X-ray crystallography at high resolution and by small-angle X-ray scattering in a solution state and via structure-based mutant studies. Biologically, YfdX was proven to be critically involved in Salmonella susceptibility to two β-lactam antibiotics, penicillin G and carbenicillin, as bacterial growth significantly impaired by its deficiency upon treatment with each of the two antibiotics was recovered by chromosomal complementation. Furthermore, by using Galleria mellonella larvae as an in vivo model of Salmonella infection, we demonstrated that Salmonella virulence was remarkably enhanced by YfdX deficiency, which was complemented by a transient expression of the wild-type or dimeric mutant but not by that of the monomeric mutant. The present study work provides direct evidence regarding the participation of YfdX in Salmonella antibiotic susceptibility and in the modulation of bacterial virulence, providing a new insight into this pathogen's strategies for survival and growth.

Structural Characteristics of Pneumolysin and Its Domains in a Biomimetic Solution

Pneumolysin (PLY) and its truncated fragments, domains 1-3 (D_1-3), and domain 4 (D₄), were purified as recombinant proteins after being cloned and over-expressed in Escherichia coli. The three-dimensional structures of these proteins were quantitatively investigated in a biomimetic condition, phosphate buffered saline (PBS) by synchrotron X-ray scattering. X-ray scattering analysis revealed important structural features including structural parameters. PLY was present as a monomeric form in PBS. The monomeric form resembled its crystallographic structure with a discrepancy of only 6.3%, confirming that PLY forms a stable structure and, thus, retains its structure in the crystalline state and even in PBS solution. D₄ was also present as a monomeric form, but its structure was very different from that of the corresponding part in the crystallographic PLY structure; the discrepancy was 92.0%. Such a dissimilar structure might originate from a less folded-chain conformation. This result suggested that the structure of D₄ is highly dependent on the crystalline or solution state and further on the presence or absence of the D_1-3 unit. In contrast, D_1-3 was dimeric rather than monomeric. Its structure was close to the most probable dimeric form of the corresponding part in the crystallographic PLY structure with 13.1% discrepancy. This fact indicated that the D_1-3 unit forms a stable structure and, indeed, such structure is well maintained in the crystalline state as well as in PBS although presented as a dimer. This result further supported that the whole structural stability of PLY is mainly attributed to the structure of D_1-3. All of PLY, D_1-3, and D₄ revealed aggregation tendencies during purification and storage. Overall, the structural characteristics of PLY and its domains in PBS may correlate to the PLY oligomer formation yielding large pore structures for the penetration of cell membranes.

Estimation of degree of polymerization of poly-acrylonitrile-grafted carbon nanotubes using Guinier plot of small angle x-ray scattering

Small angle x-ray scattering (SAXS) was used to estimate the degree of polymerization of polymer-grafted carbon nanotubes (CNTs) synthesized using a 'grafting from' method. This analysis characterizes the grafted polymer chains without cleaving them from CNTs, and provides reliable data that can complement conventional methods such as thermogravimetric analysis or transmittance electron microscopy. Acrylonitrile was polymerized from the surface of the CNTs by using redox initiation to produce poly-acrylonitrile-grafted CNTs (PAN-CNTs). Polymerization time and the initiation rate were varied to control the degree of polymerization. Radius of gyration (R _g ) of PAN-CNTs was determined using the Guinier plot obtained from SAXS solution analysis. The results showed consistent values according to the polymerization condition, up to a maximum R _g  = 125.70 Å whereas that of pristine CNTs was 99.23 Å. The dispersibility of PAN-CNTs in N,N-dimethylformamide was tested using ultraviolet-visible-near infrared spectroscopy and was confirmed to increase as the degree of polymerization increased. This analysis will be helpful to estimate the degree of polymerization of any polymer-grafted CNTs synthesized using the 'grafting from' method and to fabricate polymer/CNT composite materials.

Structural insights into the apo-structure of Cpf1 protein from Francisella novicida

Clustered regularly interspaced short palindromic repeats (CRISPRs) from Prevotella and Francisella 1 (Cpf1) are RNA-guided endonucleases that produce cohesive double-stranded breaks in DNA by specifically recognizing thymidine-rich protospacer-adjacent motif (PAM) sequences. Cpf1 is emerging as a powerful genome-editing tool. Despite previous structural studies on various Cpf1 proteins, the apo-structure of Cpf1 remains unknown. In the present study, we determined the solution structure of the Cpf1 protein from Francisella novicida (FnCpf1) with and without CRISPR RNA (crRNA) using small-angle X-ray scattering, providing the insights into the apo-structure of FnCpf1. The apo-structure of FnCpf1 was also visualized using negative staining electron microcopy. When we compared the apo-structure of FnCpf1 with crRNA-bound structure, their overall shapes (a closed form) were similar, suggesting that conformational change upon crRNA binding to FnCpf1 is not drastic, but a local induced fit might occur to recognize PAM sequences. In contrast, the apo Cpf1 from Moraxella bovoculi 237 (MbCpf1) was analyzed as an open form, implying that a large conformational change from an open to a closed form might be required for crRNA binding to MbCpf1. These results suggested that the crRNA-induced conformational changes in Cpf1 differ among species.

Architecture of the type IV coupling protein complex of Legionella pneumophila

Many bacteria, including Legionella pneumophila, rely on the type IV secretion system to translocate a repertoire of effector proteins into the hosts for their survival and growth. Type IV coupling protein (T4CP) is a hexameric ATPase that links translocating substrates to the transenvelope secretion conduit. Yet, how a large number of effector proteins are selectively recruited and processed by T4CPs remains enigmatic. DotL, the T4CP of L. pneumophila, contains an ATPase domain and a C-terminal extension whose function is unknown. Unlike T4CPs involved in plasmid DNA translocation, DotL appeared to function by forming a multiprotein complex with four other proteins. Here, we show that the C-terminal extension of DotL interacts with DotN, IcmS, IcmW and an additionally identified subunit LvgA, and that this pentameric assembly binds Legionella effector proteins. We determined the crystal structure of this assembly and built an architecture of the T4CP holocomplex by combining a homology model of the ATPase domain of DotL. The holocomplex is a hexamer of a bipartite structure composed of a membrane-proximal ATPase domain and a membrane-distal substrate-recognition assembly. The presented information demonstrates the architecture and functional dissection of the multiprotein T4CP complexes and provides important insights into their substrate recruitment and processing.

Toward redesigning the PEG surface of nanocarriers for tumor targeting: impact of inner functionalities on size, charge, multivalent binding, and biodistribution

Achieving accurate and efficacious tumor targeting with minimal off-target effects is of paramount importance in designing diagnostic and therapeutic agents for cancer. In this respect, nanocarriers have gained enormous popularity because of their attainable multifunctional features, as well as tumor-targeting potential by extravasation. However, once administered into the bloodstream, nanocarriers face various in vivo obstacles that may significantly impair their performance needed for clinical translation. Herein, we demonstrate a strategy to enhance tumor-targeting efficiency by embedding functionalities in the interior region of partially PEGylated nanocarriers (ca. 10 nm in diameter), intended for active or passive targeting. The cooperative impact of these topologically inner functional groups (IFGs) was marked: enhancements of >100-fold in IC50in vitro (e.g., a high-avidity ligand with cationic IFGs) and >2-fold in tumor accumulation at 2 h post-injection in vivo (e.g., a high-avidity ligand with anionic IFGs), both against the fully PEGylated counterpart. Analogous to allosteric modulators, properly employed IFGs may substantially improve the process of effectively directing nanocarriers to tumors, which is otherwise solely dependent on avidity or extravasation.

The role of the FliD C-terminal domain in pentamer formation and interaction with FliT

Flagellar biogenesis is controlled by a negative feedback loop. When FliD was secreted at the late step of flagellar assembly, the FliD-FliT complex disassembled and free FliT bound to the FlhDC complex, a master regulator of flagellar biogenesis, subsequently inhibiting the overall expression of flagellar proteins. In this study, we analyzed the role of the FliD C-terminal domain in pentamer formation and interaction with FliT. Our study showed that the FliD L443R mutant exists as a monomer in solution, indicating that the Leu443 residue of FliD, which contributes to its interaction with FliT, plays a crucial role in the pentameric oligomerization of FliD. Consistently, the increased levels of free FliT proteins caused by FliD L443R mutation had negative effects on the gene expression of flagellar synthesis and reduced the expression of flagellar proteins. The lengths of flagella in each cell were significantly reduced in L443R mutant strain, suggesting that normal flagellar biogenesis was impeded. These results suggest that the C-terminal domain of FliD plays a crucial role in the pentameric oligmerization of FliD and the binding of FliT to the C-terminal domain of FliD is critical to inhibit the premature assembly of the FliD pentamer in the cytosol.

Structural and functional characterization of Caenorhabditis elegans α-catenin reveals constitutive binding to β-catenin and F-actin

Intercellular epithelial junctions formed by classical cadherins, β-catenin, and the actin-binding protein α-catenin link the actin cytoskeletons of adjacent cells into a structural continuum. These assemblies transmit forces through the tissue and respond to intracellular and extracellular signals. However, the mechanisms of junctional assembly and regulation are poorly understood. Studies of cadherin-catenin assembly in a number of metazoans have revealed both similarities and unexpected differences in the biochemical properties of the cadherin·catenin complex that likely reflect the developmental and environmental requirements of different tissues and organisms. Here, we report the structural and biochemical characterization of HMP-1, the Caenorhabditis elegans α-catenin homolog, and compare it with mammalian α-catenin. HMP-1 shares overall similarity in structure and actin-binding properties, but displayed differences in conformational flexibility and allosteric regulation from mammalian α-catenin. HMP-1 bound filamentous actin with an affinity in the single micromolar range, even when complexed with the β-catenin homolog HMP-2 or when present in a complex of HMP-2 and the cadherin homolog HMR-1, indicating that HMP-1 binding to F-actin is not allosterically regulated by the HMP-2·HMR-1 complex. The middle (i.e. M) domain of HMP-1 appeared to be less conformationally flexible than mammalian α-catenin, which may underlie the dampened effect of HMP-2 binding on HMP-1 actin-binding activity compared with that of the mammalian homolog. In conclusion, our data indicate that HMP-1 constitutively binds β-catenin and F-actin, and although the overall structure and function of HMP-1 and related α-catenins are similar, the vertebrate proteins appear to be under more complex conformational regulation.

Eukaryotic Rad50 functions as a rod-shaped dimer

The Rad50 hook interface is crucial for assembly and various functions of the Mre11 complex. Previous analyses suggested that Rad50 molecules interact within (intracomplex) or between (intercomplex) dimeric complexes. In this study, we determined the structure of the human Rad50 hook and coiled-coil domains. The data suggest that the predominant structure is the intracomplex, in which the two parallel coiled coils proximal to the hook form a rod shape, and that a novel interface within the coiled-coil domains of Rad50 stabilizes the interaction of Rad50 protomers in the dimeric assembly. In yeast, removal of the coiled-coil interface compromised Tel1 activation without affecting DNA repair, while simultaneous disruption of that interface and the hook phenocopied a null mutation. The results demonstrate that the hook and coiled-coil interfaces coordinately promote intracomplex assembly and define the intracomplex as the functional form of the Mre11 complex.

Structural analyses combined with small-angle X-ray scattering reveals that the retention of heme is critical for maintaining the structure of horseradish peroxidase under denaturing conditions

We analyzed the structure of horseradish peroxidase (HRP) under denaturing conditions of 9 M urea or 6 M guanidine hydrochloride (GdnHCl). Far-UV circular dichroism (CD) spectra indicated the existence of native-like secondary structure of holo-HRP in 9 M urea. In addition, slight changes in near-UV and Soret region CD spectra of holo-HRP in 9 M urea suggest that the tertiary structure of holo-HRP and the binding of heme remain partially intact in this condition. A transition in the thermal unfolding transition curve of holo-HRP in 9 M urea indicated the existence of a considerable amount of secondary structure. However, no secondary structure, tertiary structure, or interaction between heme and HRP were observed in holo-HRP in 6 M GdnHCl. Small-angle X-ray scattering indicated that although distal and proximal domains of holo-HRP in 9 M urea might be partially unfolded, the central region that contains the heme might maintain its tertiary structure. Our results suggest that retention of the heme is essential for maintenance of the structure of HRP under highly denaturing conditions.

Tuning Oligovalent Biomacromolecular Interfaces Using Double-Layered α-Helical Coiled-Coil Nanoassemblies from Lariat-Type Building Blocks

The target affinity and selectivity of many biomacromolecules depend on the three-dimensional (3D) distribution of multiple ligands on their surfaces. Here, we devised a self-assembly strategy to control the target-tailored 3D distribution of multiple α-helical ligands on a coiled-coil core scaffold using novel lariat-type supramolecular building blocks. Depending on the coiled-coil composition and ligand grafting sites in the lariat building blocks, the structural and functional features of the self-assembled peptide nanostructures (SPNs) could be variably fine-tuned. Using oligovalent protein-RNA (Rev-RRE) interactions as a model system, we demonstrate that longer grafting reinforces the helicity of the peptide ligands, whereas shorter grafting strengthens the target binding affinity of the SPNs in both monovalent and oligovalent interactions. This supramolecular approach should be useful in developing precisely controllable multivalent ligands for biomacromolecular interactions.

Structural basis for cytokinin production by LOG from Corynebacterium glutamicum

"Lonely guy" (LOG) has been identified as a cytokinin-producing enzyme in plants and plant-interacting fungi. The gene product of Cg2612 from the soil-dwelling bacterium Corynebacterium glutamicum was annotated as an LDC. However, the facts that C. glutamicum lacks an LDC and Cg2612 has high amino acid similarity with LOG proteins suggest that Cg2612 is possibly an LOG protein. To investigate the function of Cg2612, we determined its crystal structure at a resolution of 2.3 Å. Cg2612 functions as a dimer and shows an overall structure similar to other known LOGs, such as LOGs from Arabidopsis thaliana (AtLOG), Claviceps purpurea (CpLOG), and Mycobacterium marinum (MmLOG). Cg2612 also contains a "PGGXGTXXE" motif that contributes to the formation of an active site similar to other LOGs. Moreover, biochemical studies on Cg2612 revealed that the protein has phosphoribohydrolase activity but not LDC activity. Based on these structural and biochemical studies, we propose that Cg2612 is not an LDC family enzyme, but instead belongs to the LOG family. In addition, the prenyl-binding site of Cg2612 (CgLOG) comprised residues identical to those seen in AtLOG and CpLOG, albeit dissimilar to those in MmLOG. The work provides structural and functional implications for LOG-like proteins from other microorganisms.

Synchrotron Small-Angle X-ray Scattering Study of Cross-Linked Polymeric Micelles

Polymeric micelles of methoxypoly(ethylene glycol)-b-poly(lactide) containing lysine units (mPEG-PLA-Lys4) were cross-linked by reacting of lysine moieties with a bifunctional bis(N-hydroxy-succinimide ester). The micelles were characterized in aqueous solution using dynamic light scattering, transmission electron microscopy, and synchrotron small-angle X-ray scattering. The mPEG-PLA-Lys4 was synthesized through the ring-opening polymerization of N6-carbobenzyloxy-L-lysine N-carboxyanhydride with amine-terminated mPEG-PLA and subsequent deprotection. The polymeric micelles showed enhanced micelle stability after cross-linking, which was confirmed by adding sodium dodecyl sulfate as a destabilizing agent. The average diameters measured via dynamic light scattering were 19.1 nm and 29.2 nm for non-cross-linked polymeric micelles (NCPMs) and cross-linked polymeric micelles (CPMs), respectively. The transmission electron microscopy images showed that the size of the polymeric micelles increased slightly due to cross-linking, which was in good agreement with the DLS measurements. The overall structures and internal structural changes of NCPMs and CPMs in aqueous solution were studied in detail using synchrotron X-ray scattering method. According to the structural parameters of X-ray scattering analysis, CPMs with a more densely packed core structure were formed by reacting bifunctional cross-linking agents with lysine amino groups located in the innermost core of the polymeric micelles.

Small angle X-ray scattering studies of CTNNBL1 dimerization and CTNNBL1/CDC5L complex

The hPrp19/CDC5L complex is a non-snRNP spliceosome complex that plays a key role in the spliceosome activation during pre-mRNA splicing, and CTNNBL1 and CDC5L are essential components of the complex. In this study, to investigate the oligomeric state of CTNNBL1 in solution, we performed small angle X-ray scattering experiments in various concentrations of NaCl. We observed that CTNNBL1 existed as a dimer in physiological NaCl concentrations. Site-directed mutagenesis experiment of CTNNBL1 confirmed that N-terminal capping region and the first four ARM repeats are important for dimerization of the protein. We also found that the positively-charged NLS3-containing region (residues 197-235) of CDC5L bound to the negatively-charged patch of CTNNBL1 and that the CTNNBL1/CDC5L complex formed a heterotetramer consisting of one CTNNBL1 dimer and one CDC5L dimer. Moreover, reconstruction of 3D models of CTNNBL1/CDC5L complexes containing CTNNBL1 and three different truncated forms of CDC5L showed that the CDC5L(141-196) region and the CDC5L(236-377) region were positioned at the top of the N-terminal capping region and at the bottom of ARM VII of CTNNBL1, respectively.

A Simple Evaporation Method for Large-Scale Production of Liquid Crystalline Lipid Nanoparticles with Various Internal Structures

We present a simple and industrially accessible method of producing liquid crystalline lipid nanoparticles with various internal structures based on phytantriol, Pluronic F127, and vitamin E acetate. Bilayer vesicles were produced when an ethanolic solution dissolving the lipid components was mixed with deionized water. After the evaporation of ethanol from the aqueous mixture, vesicles were transformed into lipid-filled liquid crystalline nanoparticles with well-defined internal structures such as hexagonal lattices (mostly inverted cubic Pn3m), lined or coiled pattern (inverted hexagonal H2), and disordered structure (inverse microemulsion, L2), depending on the compositions. Further studies suggested that their internal structures were also affected by temperature. The internal structures were characterized from cryo-TEM and small-angle X-ray scattering results. Microcalorimetry studies were performed to investigate the degree of molecular ordering/crystallinity of lipid components within the nanostructures. From the comparative studies, we demonstrated the present method could produce the lipid nanoparticles with similar characteristics to those made from a conventional method. More importantly, the production only requires simple tools for mixing and ethanol evaporation and it is possible to produce 10 kg or so per batch of aqueous lipid nanoparticles dispersions, enabling the large-scale production of the liquid crystalline nanoparticles for various biomedical applications.

Amyloid fibrillation of insulin under water-limited conditions

Amyloid fibrillation in water-organic mixtures has been widely studied to understand the effect of protein-solvent interactions on the fibrillation process. In this study, we monitored insulin fibrillation in formamide and its methyl derivatives (formamide, N-methyl formamide, N,N-dimethyl formamide) in the presence and absence of water. These model solvent systems mimic the cellular environment by providing denaturing conditions and a hydrophobic environment with limited water content. Thioflavin T (ThT) assay revealed that binary mixtures of water with formamide and its methyl derivatives enhanced fibrillation rates and ?-sheet abundance, whereas organic solvents suppressed insulin fibrillation. We utilized solution small-angle x-ray scattering (SAXS) and differential scanning calorimetry (DSC) to investigate the correlation between protein-solvent interactions and insulin fibrillation. SAXS experiments combined with simulated annealing of the protein indicated that the degree of denaturation of the hydrophobic core region at residues B11-B17 determines the fibrillation rate. In addition, DSC experiments suggested a crucial role of hydrophobic interactions in the fibrillation process. These results imply that an environment with limited water, which imitates a lipid membrane system, accelerates protein denaturation and the formation of intermolecular hydrophobic interactions during amyloid fibrillation.

Molecular basis for SMC rod formation and its dissolution upon DNA binding

SMC condensin complexes are central modulators of chromosome superstructure in all branches of life. Their SMC subunits form a long intramolecular coiled coil, which connects a constitutive “hinge” dimerization domain with an ATP-regulated “head” dimerization module. Here, we address the structural arrangement of the long coiled coils in SMC complexes. We unequivocally show that prokaryotic Smc-ScpAB, eukaryotic condensin, and possibly also cohesin form rod-like structures, with their coiled coils being closely juxtaposed and accurately anchored to the hinge. Upon ATP-induced binding of DNA to the hinge, however, Smc switches to a more open configuration. Our data suggest that a long-distance structural transition is transmitted from the Smc head domains to regulate Smc-ScpAB’s association with DNA. These findings uncover a conserved architectural theme in SMC complexes, provide a mechanistic basis for Smc’s dynamic engagement with chromosomes, and offer a molecular explanation for defects in Cornelia de Lange syndrome.

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Prokaryotic Smc-ScpAB complexes form rod-like structures

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Binding of ATP and DNA induces a rod-to-ring transition in prokaryotic condensin

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The condensin hinge is rigidly anchored to its coiled coil

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The rod-like conformation is a conserved feature of SMC protein dimers