Search Results (109)

AAA+ ATPases are ring-shaped hexameric protein complexes that operate as elaborate macromolecular motors, driving a variety of ATP-dependent cellular processes. AAA+ ATPases undergo large-scale conformational changes that lead to the conversion of chemical energy from ATP into mechanical work to perform a wide range of functions, such as unfolding and translocation of the protein substrate inside a proteolysis chamber of an AAA+-associated protease. Despite extensive biochemical studies on these macromolecular assemblies, the mechanism of substrate unfolding and degradation has long remained elusive. Indeed, until recently, structural characterization of AAA+ protease complexes remained hampered by the size and complexity of the machinery, harboring multiple protein subunits acting together to process proteins to be degraded. Additionally, the major structural rearrangements involved in the mechanism of this complex represent a crucial challenge for structural biology. Here, we report the main advances in deciphering molecular details of the proteolytic reaction performed by AAA+ proteases, based on the remarkable progress in structural biology techniques. Particular emphasis is placed on the latest findings from high-resolution structural analysis of the ClpXP proteolytic complex, using crystallographic and cryo-EM investigations. In addition, this review presents some additional dynamic information obtained using solution-state NMR. This information provides molecular details that help to explain the protein degradation process by such molecular machines. Full article

The cationic chloro-P-{[4-(diphenylphosphanyl)phenyl]-N,N-dimethylmethanammonio(norbornadiene)rhodium(I) complex was encapsulated inside a self-assembled hexameric capsule. This capsule was obtained through a reaction involving 2,8,14,20-tetra-undecyl-resorcin[4]arene and water in chloroform. The formation of an inclusion complex was deduced from a combination of spectral measurements (UV-visible spectroscopy, ¹H, ³¹P{¹H} NMR and DOSY). The rhodium complex was evaluated in the [2+2+2] cycloaddition between N,N-dipropargyl-p-toluenesulfonamide and arylacetylene derivatives. In the presence of two equivalents of arylacetylenes in water-saturated chloroform at 60 °C for 24 h, the 4-methyl-N-(prop-2-yn-1-yl)-N-((2-tosylisoindolin-5-yl)methyl)benzenesulfonamide, the homocycloaddition product of 1,6-diyne is predominantly formed. In the presence of the supramolecular capsule, a selectivity inversion in favor of 5-aryl-2-tosylisoindoline is observed, with heterocycloaddition products formed in proportions between 53 and 69%. Full article

The [PdCl₂(cod)] complex was encapsulated inside a self-assembled hexameric capsule obtained via a reaction of 2,8,14,20-tetra-undecyl-resorcin[4]arene and water. The formation of an inclusion complex was deduced from a combination of spectral measurements (UV-visible, ¹H NMR and DOSY spectroscopies). The latter proved effective in the dimerization of styrene derivatives under mild conditions, with a catalyst loading of 0.5 mol% at 60 °C. Electronically enriched vinyl arenes underwent cyclization of the catalytic products, leading to the quasi-quantitative formation of indanes from 4-tert-butylstyrene and 9-vinylanthracene. In the instance of 9-vinylanthracene, the rearrangement product is tribenzo–pentaphene, which is formed in 50% of conversions. Full article

The HIV-1 capsid is one of virology’s most iconic structures, yet how it assembles has long remained elusive. Remarkably, the capsid is made from just a single protein, CA, which forms a lattice of ~250 hexamers and exactly 12 pentamers. Conical capsids form inside budded virions during maturation, but early efforts to reproduce this in vitro resulted instead in open-ended tubes with a purely hexameric lattice. The missing component in capsid assembly was finally identified as the metabolite inositol hexakisphosphate (IP6). Simply mixing soluble CA protein with IP6 is sufficient to drive the spontaneous assembly of conical capsids with a similar size and shape to those inside of infectious virions. Equally important, IP6 stabilises capsids once formed, increasing their stability from minutes to hours. Indeed, such is the dependence of HIV-1 on IP6 that the virus actively packages it into virions during production. These discoveries have stimulated work from multiple labs into the role and importance of IP6 in HIV-1 replication, and is the subject of this review. Full article

Hemocyanins are oxygen-transporting proteins found in crustaceans and other arthropods, playing key roles in immune defense and metabolic regulation. Due to their stability and bioactive properties, Hcs have gained increasing interest in biotechnological and biomedical applications. However, detailed biophysical characterization is crucial to understanding their functional potential. In this study, the hemocyanin was extracted and purified from Macrobrachium acanthurus (HcMac) using ultracentrifugation and size-exclusion chromatography. The molecular mass of HcMac was determined by SDS-PAGE electrophoresis, MALDI-TOF mass spectrometry, and analytical ultracentrifugation. Spectroscopic analyses, including UV-Vis absorption, fluorescence emission, and light scattering intensity, were used to assess the structural stability of the compound under various pH conditions. HcMac was identified as a hexameric protein (~450 kDa) composed of monomeric subunits of 75 and 76 kDa. The protein maintained its oligomeric stability and oxygen-binding affinity in the pH range of 5.0–7.4. However, extreme pH conditions (below 4.4 and above 7.5) induced structural alterations, leading to dissociation and conformational changes, as evidenced by fluorescence emission and UV-Vis spectra. The isoelectric point was determined to be between pH 4.3 and 5.3, consistent with other crustacean HCs. These findings reinforce the structural robustness of HcMac and suggest its potential for biotechnological applications. The high stability of HcMac under physiological pH conditions indicates its suitability for biomedical research, including immunomodulatory and antimicrobial applications. Future studies integrating bioinformatics, proteomics, and immunological assays will be essential to explore the therapeutic potential of HcMac. Full article

Perfringolysin O (PFO) is a prototypical member of a large family of pore-forming toxins (PFTs) that are potent virulence factors for many pathogenic bacteria. One of the most enigmatic properties of these PFTs is how structural changes are coordinated between different subunits within a single complex. Moreover, there are conflicting data in the literature, with gel electrophoresis results apparently showing that pores are only complete rings, whereas microscopy images clearly also show incomplete-ring pores. Here, we developed a novel multi-stack gel electrophoretic assay to finely separate PFO pore complexes and found that this assay indeed resolves both complete- and incomplete-ring pores. However, unexpectedly, we found that the stoichiometries of these complexes are predominantly integral multiples of six subunits. High-resolution atomic force microscopy images of PFO pore complexes also reveal a predominant hexameric-based stoichiometry. We also observed this hexameric-based stoichiometry at the prepore stage and identified a mutant that is kinetically trapped at a hexameric state. Thus, overall, these results reveal a previously unknown hexameric-based structural hierarchy in the PFO complexes. We suggest that the structural coordination within the hexamers is different than between the hexamers and is thus a critical feature of the structural coordination of the complex as a whole. Full article

It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of siphophages remain scarce. Using cryo-EM, we resolved the structures of T-series siphophage T1, encompassing its head, connector complex, tail tube, and tail tip, at near-atomic resolution. The density maps enabled us to build the atomic models for the majority of T1 proteins. The T1 head comprises 415 copies of the major capsid protein gp47, arranged into an icosahedron with a triangulation number of seven, decorated with 80 homologous trimers and 60 heterotrimers along the threefold and quasi-threefold axes of the icosahedron. The T1 connector complex is composed of two dodecamers (a portal and an adaptor) and two hexamers (a stopper and a tail terminator). The flexible tail tube comprises approximately 34 hexameric rings of tail tube. The extensive disulfide bond network along the successive tail rings may mediate the flexible bending. The distal tip of T1, which is cone-shaped and assembled by proteins gp33, gp34, gp36, gp37, and gp38, displays structural similarity to that of phage lambda. In conjunction with previous studies of lambda-like siphophages, our structure will facilitate further exploration of the structural and mechanistic aspects of lambda-like siphophages. Full article

CD137 is a prominent costimulatory molecule of the tumor necrosis factor (TNF) receptor superfamily that activates T cells through a complex bidirectional signaling process involving CD137L. The clinical value of immunotherapies underscores the potential of CD137L/CD137 as an effective target for boosting antitumor immune responses; however, the intricate mechanisms governing these interactions have not been fully elucidated. Herein, we constructed various oligomeric states of CD137L (monomeric, dimeric, and trimeric CD137L) and explored their interactions with CD137 using molecular dynamics simulations. Our findings revealed that trimeric CD137L exhibits higher thermal stability but reduced binding affinity for CD137 compared with the dimer form, with the A’B’ loop of CD137L playing a critical role in both structural stability and promoting CD137 interactions. Notably, the formation of hexameric structures enhanced the binding affinity and stability. This study provides valuable insights into the CD137L/CD137 bidirectional signaling mechanisms, which may inform the design of next-generation CD137 agonists. Ultimately, these advancements may improve cancer immunotherapy strategies, aiming to enhance therapeutic outcomes for patients through more effective and targeted therapies. Full article

The kinetic stability provided by the sterically demanding {SiN^Dipp}²⁻ dianion (SiN^Dipp = {CH₂SiMe₂NDipp}₂; Dipp = 2,6-i-Pr₂C₆H₃) is intrinsic to the isolation of not only the group 1 alumanyl reagents ([{SiN^Dipp}AlM]₂; M = K, Rb, Cs) but also facilitates the completely selective oxidative addition of a C-H bond of 1,2-C₂B₁₀H₁₂ to the aluminium centre. In each case, the resultant compounds comprise a four-coordinate o-carboranyl (hydrido)aluminate anion, [(SiN^Dipp)Al(H)(1,2-C₂B₁₀H₁₁)]⁻, in which the carboranyl cage is bonded to aluminium by an Al-C σ bond. Although the anions further assemble as extended network structures based on Al-H∙∙∙M, B-H∙∙∙M, and C-H∙∙∙M interactions, each structure is unique due to the significant variation in M⁺ ionic radius as group 1 is descended. The potassium derivative crystallises as a one-dimensional polymer, its rubidium analogue is a dimer due to the polyhapto-sequestration of a molecule of benzene solvent within the alkali metal coordination sphere, and the caesium species is a two-dimensional assembly of hexameric aggregates. Full article

Serum amyloid A (SAA) is a small protein consisting of 104 residues and, under physiological conditions, exists mainly in hexameric form. It belongs to the positive acute-phase proteins, which means that its plasma concentration increases rapidly in response to injury, inflammation, and infection. The accumulation of SAA molecules promotes the formation of amyloid aggregates, which deposit extracellularly in many organs, causing their dysfunction. In our previous work, we successfully designed a peptidomimetic that inhibited the aggregation of amyloidogenic SAA fragments. In the present paper, we show how the same inhibitor, named saa3Dip, affects the oligomerization and aggregation processes of MetSAA1.1 protein. The thioflavin T assay showed that saa3Dip inhibited its fibrillization. The measurement of the internal fluorophore fluorescence (Trp) showed differences that occurred in the tertiary structure of MetSAA1.1 in the presence of the inhibitor, which was also confirmed by CD spectra in the aromatic range. FTIR results suggested that saa3Dip could stabilize some fragments of the native structure of MetSAA1.1, which was confirmed by determining the melting temperature (Tm) of the protein–inhibitor complex. AFM images demonstrated that the presence of saa3Dip prevented the formation of large SAA aggregates. Our results suggest that saa3Dip stabilizes the native conformation of MetSAA1.1. Full article

We isolated a stress-tolerance-related gene from a genome library of Synechococcus sp. NKBG15041c. The expression of the gene in E. coli confers resistance against various stresses. The gene encodes a MoxR AAA+ ATPase, which was designated SyMRP since it belongs to the MRP subfamily. The recombinant SyMRP showed weak ATPase activity and protected citrate synthase from thermal aggregation. Interestingly, the chaperone activity of SyMRP is ATP-dependent. SyMRP exists as a stable hexamer, and ATP-dependent conformation changes were not detected via analytical ultracentrifugation (AUC) or small-angle X-ray scattering (SAXS). Although the hexameric structure predicted by AlphaFold 3 was the canonical flat-ring structure, the structures observed by atomic force microscopy (AFM) and transmission electron microscopy (TEM) were not the canonical ring structure. In addition, the experimental SAXS profiles did not show a peak that should exist in the symmetric-ring structure. Therefore, SyMRP seems to form a hexameric structure different from the canonical hexameric structure of AAA+ ATPase. Full article

The steric hindrance in molecules of 1-(2,4,6-trimethylphenyl)ethanone and 1-(2,4,6-triisopropylphenyl)ethanone were shown to substantially differentiate the options of synthesis of the respective alcohols. The former was obtained with a yield of 12% with a mild reducing agent, i.e., NaBH₄, as well as in vapor phase transfer hydrogenation (22% yield at 673 K) over MgO, whereas the latter was not formed at all under those conditions. The only agent that was able to reduce both ketones was LiAlH₄. The single crystals of the two alcohols were obtained and their structures were determined. The symmetry of the 0-D hydrogen-bonded networks of molecules in these crystals was analyzed. It was shown that the methyl substituent allows the molecules to form hexameric rings, whereas the isopropyl-substituted molecules formed tetrameric ones. In both cases, there were two types of rings in the cell, but four types of molecules forming tetramers and only three types of molecules in the hexamers. These structures were compared to similar structures formed by other molecules found in the Cambridge Structural Database via hydrogen bonding. Moreover, the single crystal of 1-(2,4,6-triisopropylphenyl)ethanone was obtained to explain if either the hydrogen bonding or the presence of isopropyl groups influences the angles in the molecules. Full article

In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol hexakisphosphate, an assembly and stability factor for the capsid. Previously, it was shown that amino-acid substitutions of Arg18 can promote pentamer incorporation into capsid-like particles (CLPs) that spontaneously assemble in vitro under high-salt conditions. Here, we show that these Arg18 mutant CLPs contain a non-canonical pentamer conformation and distinct lattice characteristics that do not follow the fullerene geometry of retroviral capsids. The Arg18 mutant pentamers resemble the hexamer in intra-oligomeric contacts and form a unique tetramer-of-pentamers that allows for incorporation of an octahedral vertex with a cross-shaped opening in the hexagonal capsid lattice. Our findings highlight an unexpected degree of structural plasticity in HIV-1 capsid assembly. Full article

The interaction between IgM and C1q represents the first step of the classical pathway of the complement system in higher vertebrates. To identify the significance of particular IgM/C1q interactions, recombinant IgMs were used in both hexameric and pentameric configurations and with two different specificities, along with C1q derived from human serum (sC1q) and two recombinant single-chain variants of the trimeric globular region of C1q. Interaction and complement activation assays were performed using the ELISA format, and bio-layer interferometry measurements to study kinetic behavior. The differences between hexameric and pentameric IgM conformations were only slightly visible in the interaction assay, but significant in the complement activation assay. Hexameric IgM requires a lower concentration of sC1q to activate the complement compared to pentameric IgM, leading to an increased release of C4 compared to pentameric IgM. The recombinant C1q mimetics competed with sC1q in interaction assays and were able to inhibit complement activation. The bio-layer interferometry measurements revealed K_D values in the nanomolar range for the IgM/C1q interaction, while the C1q mimetics exhibited rapid on and off binding rates with the IgMs. Our results make C1q mimetics valuable tools for developing recombinant C1q, specifically its variants, for further scientific studies and clinical applications. Full article

Two new Mn(II) and Zn(II) metal–organic compounds of 1,10-phenanthroline and methyl benzoates viz. [Mn(phen)₂Cl₂]2-ClBzH (1) and [Zn(4-MeBz)₂(2-AmPy)₂] (2) (where 4-MeBz = 4-methylbenzoate, 2-AmPy = 2-aminopyridine, phen = 1,10-phenanthroline, 2-ClBzH = 2-chlorobenzoic acid) were synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR, electronic) and single crystal X-ray diffraction techniques. The crystal structure analysis of the compounds revealed the presence of various non-covalent interactions, which provides stability to the crystal structures. The crystal structure analysis of compound 1 revealed the formation of a supramolecular dimer of 2-ClBzH enclathrate within the hexameric host cavity formed by the neighboring monomeric units. Compound 2 is a mononuclear compound of Zn(II) where flexible binding topologies of 4-CH₃Bz are observed with the metal center. Moreover, various non-covalent interactions, such as lp(O)-π, lp(Cl)-π, C–H∙∙∙Cl, π-stacking interactions as well as N–H∙∙∙O, C–H∙∙∙O and C–H∙∙∙π hydrogen bonding interactions, are found to be involved in plateauing the molecular self-association of the compounds. The remarkable enclathration of the H-bonded 2-ClBzH dimer into a supramolecular cavity formed by two [Mn(phen)₂Cl₂] complexes were further studied theoretically using density functional theory (DFT) calculations, the non-covalent interaction (NCI) plot index and quantum theory of atoms in molecules (QTAIM) computational tools. Synergistic effects were also analyzed using molecular electrostatic potential (MEP) surface analysis. Full article