Mechanism Of Oligomerization Research Articles

Power of protein/tRNA functional assembly against aberrant aggregation.

Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis. Here, we show that TrmFO carries an unstable protein structure that can partially mis-unfold leading to either formation of irregular and nonfunctional soluble oligomers endowed with hyper-thermal stability or large amorphous aggregates in the presence of salts. Mutagenesis confirmed that this peculiarity is an intrinsic property of a polypeptide and it is independent of the flavin coenzyme. Structural characterization and kinetic studies identified several regions of the protein that enjoy conformational changes and more particularly pinpointed the N-terminal subdomain as being a key element in the mechanisms of oligomerization and aggregation. Only stabilization of this region via tRNA suppresses these aberrant protein states. Although protein chaperones emerged as major actors against aggregation, our study emphasizes that other powerful mechanisms exist such as the stabilizing effect of functional assemblies that provide an additional layer of protection against the instability of the proteome.

Separate mechanisms of ion oligomerization tune the physicochemical properties of n-butylammonium acetate: cation-base clusters vs. anion-acid dimers.

We investigated the ability of the ions comprising protic ionic liquids to strongly interact with their neutral acid and base forms through the characterization of n-butylammonium acetate ([C4NH3][OAc]) in the presence of excess n-butylamine (C4NH2) or excess acetic acid (HOAc). The conjugate and parent acid or base form new nonstoichiometric, noncovalently bound species (i.e., oligomeric ions) which change the physical and chemical properties of the resulting liquids, thus offering tunability. The effects of adding C4NH2 or HOAc to [C4NH3][OAc] on the resulting thermal and spectroscopic properties differ and suggest that C4NH2 interacts primarily with [C4NH3]+ to form 3-dimensional polymeric networks likely similar to those in H2O/[H3O]+, while HOAc interacts primarily with [OAc]- to form oligomeric ions (e.g., [H(OAc)2]-). The densities of the systems increased with the increase of acid content and reached a maximum when the acid molar fraction was 0.90, but decreased with increasing amine concentration. The viscosities decreased significantly with increasing acid or base concentration. The solvent properties of the mixtures were assessed by measuring the solubilities of benzene, ethyl acetate, diethyl ether, heptane, ibuprofen free acid, and lidocaine free base. The solubilities of the organic solutes and active pharmaceutical ingredients can be tuned with the concentration of acid or amine in the mixtures. In addition, crystallization of the active pharmaceutical ingredients can be induced with the modification of the composition of the mixtures. These observations support the usage of these mixtures for the synthesis and purification of acid or basic active pharmaceutical ingredients in the pharmaceutical industry.

Structural and thermodynamical properties of early human amylin oligomers using replica exchange molecular dynamics: mutation effect of three key residues F15, H18 and F23.

Human islet amyloid polypeptide (hIAPP) is a 37-residue polypeptide, considered to be the main component of the pancreatic islet amyloid associated with type 2 diabetes and is one of the most amyloidogenic polypeptides known. Although the structure of hIAPP fibrils has already been obtained, structures of early oligomers and the mechanism of β-sheet formation remain poorly understood. Herein, we characterize the atomic structure and the thermodynamics of the 14-37 residue fragment of hIAPP wild-type and mutated dimers and trimers. More precisely, three key residues, F15, H18 and F23, thought to affect the aggregation process, are the focus of this numerical study using replica exchange molecular dynamics coupled with the OPEP coarse-grained protein force field. Our simulations show that the oligomerization process takes place through the formation of anti-parallel β-sheets most probably between C-terminal regions. Two main characteristics are associated with the onset of the fibrillation process. First, the sequence matching between the central (20-29) and C-terminal (30-37) regions, at intra and inter-molecular levels, helps in stabilizing the secondary structure and facilitates intermolecular interactions. Second, hydrophobic residues I26 and L27 are likely to promote the capture of further oligomeric structures and thus facilitate fibril elongation. Histidine mutation should have a more pronounced effect in the N-terminal region while phenylalanine mutations do not seem to prevent amyloid formation since central/C-terminal interactions are conserved through other contacts.

Human cystatin C monomer, dimer, oligomer, and amyloid structures are related to health and disease.

Human cystatin C (hCC) is a small protein belonging to the cystatin family of papain-like cysteine proteinase inhibitors. We review the recent literature concerning structural aspects of hCC related to disease. We focus on the mechanisms of hCC dimerization, oligomerization, and amyloid formation. Amyloid formation is associated with a number of neurodegenerative diseases that affect the independence and quality of life of aging populations. hCC is one of the second-wave proteins that have been found to undergo amyloidosis associated with disease. For hCC, this includes cerebral amyloid angiopathy, as well as a disorder resulting in reduced male fertility.

Structural Dynamics of the Vimentin Coiled-coil Contact Regions Involved in Filament Assembly as Revealed by Hydrogen-Deuterium Exchange

Intermediate filaments (IF) are major constituents of the cytoskeleton of metazoan cells. They are not only responsible for the mechanical properties but also for various physiological activities in different cells and tissues. The building blocks of IFs are extended coiled-coil-forming proteins exhibiting a characteristic central α-helical domain ("rod"). The fundamental principles of the filament assembly mechanism and the network formation have been widely elucidated for the cytoplasmic IF protein vimentin. Also, a comprehensive structural model for the tetrameric complex of vimentin has been obtained by X-ray crystallography in combination with various biochemical and biophysical techniques. To extend these static data and to investigate the dynamic properties of the full-length proteins in solution during the various assembly steps, we analyzed the patterns of hydrogen-deuterium exchange in vimentin and in four variants carrying point mutations in the IF consensus motifs present at either end of the α-helical rod that cause an assembly arrest at the unit-length filament (ULF) stage. The results yielded unique insights into the structural properties of subdomains within the full-length vimentin, in particular in regions of contact in α-helical and linker segments that stabilize different oligomeric forms such as tetramers, ULFs, and mature filaments. Moreover, hydrogen-deuterium exchange analysis of the point-mutated variants directly demonstrated the active role of the IF consensus motifs in the oligomerization mechanism of tetramers during ULF formation. Ultimately, using molecular dynamics simulation procedures, we provide a structural model for the subdomain-mediated tetramer/tetramer interaction via "cross-coiling" as the first step of the assembly process.

Theoretical study on the oligomerization mechanisms of bihydroxysilicone.

Bihydroxysilicone SiO(OH)2 is the simplest silicone monomer and can be condensed to various silica materials with diverse properties. The oligomerization mechanisms of SiO(OH)2 were investigated systematically at B3LYP/6-311++G(d,p) level. All species including the monomers, dimers, trimers, and tetramers were fully optimized with CPCM solvation model to simulate the solvent environments in methanol. The Si=O bonds of silicones can couple via barrierless processes to form varied ringed structures, and bigger rings can be formed by dehydration and recyclization. The most stable trimer is the one with a hexagonal Si-O ring, and the energetically most favorable tetramer is the one with an octagonal Si-O ring and two hydroxyl groups on each Si atom. Graphical Abstract Selected oligomers in the oligomerization mechanisms of bihydroxysiliconeᅟ.

Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.

3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

Death Domain Signaling by Disulfide-Linked Dimers of the p75 Neurotrophin Receptor Mediates Neuronal Death in the CNS

The p75 neurotrophin receptor (p75(NTR)) mediates neuronal death in response to neural insults by activating a caspase apoptotic pathway. The oligomeric state and activation mechanism that enable p75(NTR) to mediate these effects have recently been called into question. Here, we have investigated mutant mice lacking the p75(NTR) death domain (DD) or a highly conserved transmembrane (TM) cysteine residue (Cys(259)) implicated in receptor dimerization and activation. Neuronal death induced by proneurotrophins or epileptic seizures was assessed and compared with responses in p75(NTR) knock-out mice and wild-type animals. Proneurotrophins induced apoptosis of cultured hippocampal and cortical neurons from wild-type mice, but mutant neurons lacking p75(NTR), only the p75(NTR) DD, or just Cys(259) were all equally resistant to proneurotrophin-induced neuronal death. Homo-FRET anisotropy experiments demonstrated that both NGF and proNGF induce conformational changes in p75(NTR) that are dependent on the TM cysteine. In vivo, neuronal death induced by pilocarpine-mediated seizures was significantly reduced in the hippocampus and somatosensory, piriform, and entorhinal cortices of all three strains of p75(NTR) mutant mice. Interestingly, the levels of protection observed in mice lacking the DD or only Cys(259) were identical to those of p75(NTR) knock-out mice even though the Cys(259) mutant differed from the wild-type receptor in only one amino acid residue. We conclude that, both in vitro and in vivo, neuronal death induced by p75(NTR) requires the DD and TM Cys(259), supporting the physiological relevance of DD signaling by disulfide-linked dimers of p75(NTR) in the CNS. A detailed understanding of the physiological significance of distinct structural determinants in the p75 neurotrophin receptor (p75(NTR)) is crucial for the identification of suitable drug targets in this receptor. We have tested the relevance of the p75(NTR) death domain (DD) and the highly conserved transmembrane residue Cys(259) for the ability of p75(NTR) to induce apoptosis in neurons of the CNS using gene-targeted mutant mice. The physiological importance of these determinants had been contested in some recent in vitro studies. Our results indicate a requirement for DD signaling by disulfide-linked dimers of p75(NTR) for neuronal death induced by proneurotrophins and epileptic seizures. These new mouse models will be useful for clarifying different aspects of p75(NTR) physiology.

Reaction Mechanisms of the Initial Oligomerization of Aluminophosphate

The mechanisms of aluminophosphate oligomerization were investigated using density functional theory with the SMD solvation model. Two aluminum species, Al(OH)4(-) and Al(H2O)6(3+), and four phosphorus species, H3PO4, H2PO4(-), HPO4(2-), and PO4(3-), were considered as the monomers for polycondensation reactions. It was found that the most favorable pathway to dimerization was a Lewis acid-base reaction: the aprotic oxygen of phosphoric acid (P═O) performs a nucleophilic attack on the central aluminum atom of Al(OH)4(-). Using this mechanism as a pattern, plausible dimerization mechanisms were investigated by varying the proticity and hydration of the phosphorus and aluminum monomers, respectively. The relative reaction rates of each mechanism were estimated under different pH conditions. The chain growth of aluminophosphates to trimers, tetramers, and pentamers and the cyclization of a linear tetramer were also investigated. For oligomerization reactions beyond dimer formation, it is found that cluster growth favors the addition of the phosphoric monomers rather than aluminum monomers.

Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product

Bacteriophages produce endolysins, which lyse the bacterial host cell to release newly produced virions. The timing of lysis is regulated and is thought to involve the activation of a molecular switch. We present a crystal structure of the activated endolysin CTP1L that targets Clostridium tyrobutyricum, consisting of a complex between the full-length protein and an N-terminally truncated C-terminal cell wall binding domain (CBD). The truncated CBD is produced through an internal translation start site within the endolysin gene. Mutants affecting the internal translation site change the oligomeric state of the endolysin and reduce lytic activity. The activity can be modulated by reconstitution of the full-length endolysin-CBD complex with free CBD. The same oligomerization mechanism applies to the CD27L endolysin that targets Clostridium difficile and the CS74L endolysin that targets Clostridium sporogenes. When the CTP1L endolysin gene is introduced into the commensal bacterium Lactococcus lactis, the truncated CBD is also produced, showing that the alternative start codon can be used in other bacterial species. The identification of a translational switch affecting oligomerization presented here has implications for the design of effective endolysins for the treatment of bacterial infections.

Unraveling the Molecular Mechanism of pH-Induced Misfolding and Oligomerization of the Prion Protein

The misfolding of the prion protein (PrP) to aggregated forms is linked to several neurodegenerative diseases. Misfolded oligomeric forms of PrP are associated with neurotoxicity and/or infectivity, but the molecular mechanism by which they form is still poorly understood. A reduction in pH is known to be a key factor that triggers misfolded oligomer formation by PrP, but the residues whose protonation is linked with misfolding remain unidentified. The structural consequences of the protonation of these residues also remain to be determined. In the current study, amino acid residues whose protonation is critical for PrP misfolding and oligomerization have been identified using site-directed mutagenesis and misfolding/oligomerization assays. It is shown that the protonation of either H186 or D201, which mimics the effects of pathogenic mutations (H186R and D201N) at both residue sites, is critically linked to the stability, misfolding and oligomerization of PrP. Hydrogen–deuterium exchange studies coupled with mass spectrometry show that the protonation of either H186 or D201 leads to the same common structural change: increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2. It is shown that the protonation of either of these residues is sufficient for accelerating misfolded oligomer formation, most likely because the protonation of either residue causes the same structural perturbation. Hence, the increased structural dynamics in helix 1 and that in the loop between helix 1 and β-strand 2 appear to play an early critical role in acid-induced misfolding of PrP.

Oligomeric Structures of an Aggregation-Triggering Fragment of SOD1 Protein

Abstract: Amyloid fibril formation of copper-zinc superoxide dismutase (SOD1) is linked to familial amyotrophic lateral sclerosis (fALS), a progressive neurodegenerative disease. A recent experimental study has shown that 147GVIGIAQ153 peptide of the SOD1 C-terminal segment can form amyloid fibril and also accelerate the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks fibril formation of this peptide. However, the oligomeric structure and aggregation mechanism of this fragment remain elusive. In this study, we have investigated the hexameric structures of GVIGIAQ and its I149P variant by performing extensive atomistic explicit-solvent replica exchange molecular dynamics (REMD) simulations. We found that the GVIGIAQ hexamers adopt various β-sheet-rich conformations, including disordered aggregates and, to a much lesser extent, ordered fibril-like bilayer β-sheets and β-barrels. Structural analysis shows that four-stranded monolayer β-sheets are the smallest β-sheets that can form both bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability of all residues, especially those close to I149 in amino acid sequence, thus resulting in the vanish of bilayer β-sheets, a decrease of β-barrels, and a dramatic increase of disordered aggregates. The lack of bilayer β-sheets provides an explanation for the experimental observation of no fibril formation for I149P variant. MD simulation results on the structural stability of different sizes of experimental bilayer β-sheet fibril models further support the importance of I149 on fibril formation and also suggest that the bilayer β-sheet consisting of eight chains might be the smallest nucleus for 147GVIGIAQ153 fibril formation.

Ethene Oligomerization in Ni-Containing Zeolites: Theoretical Discrimination of Reaction Mechanisms

Ni-containing porous aluminosilicates are promising heterogeneous catalysts for oligomerization of ethene, but little is known about the catalytic cycle. In addition, it remains unclear why the aluminosilicates work without the alkyl aluminum cocatalyst needed in homogeneous catalysis. As the first of its kind, this work uses density functional theory (DFT) to identify the most probable mechanism of oligomerization and active site formation. The periodic DFT calculations employed the BEEF-vdW functional to consider both short-range interactions involved in bond formation and long-range interactions with the zeolite framework. The calculations targeted Ni-containing SSZ-24 zeolite as a representative catalyst and considered Ni+, Ni2+ ions, and neutral nickel atoms as active sites. We investigated the catalytic cycles of the metallacycle and Cossee–Arlman mechanisms that have been proposed in the literature, in addition to a new proton-transfer mechanism. Free energy profiles were derived at a typical exper...

A qualitative comparison of secondary organic aerosol yields and composition from ozonolysis of monoterpenes at varying concentrations of NO<sub>2</sub>

Abstract. The effect of NO2 on secondary organic aerosol (SOA) formation from ozonolysis of α-pinene, β-pinene, Δ3-carene, and limonene was investigated using a dark flow-through reaction chamber. SOA mass yields were calculated for each monoterpene from ozonolysis with varying NO2 concentrations. Kinetics modeling of the first-generation gas-phase chemistry suggests that differences in observed aerosol yields for different NO2 concentrations are consistent with NO3 formation and subsequent competition between O3 and NO3 to oxidize each monoterpene. α-Pinene was the only monoterpene studied that showed a systematic decrease in both aerosol number concentration and mass concentration with increasing [NO2]. β-Pinene and Δ3-carene produced fewer particles at higher [NO2], but both retained moderate mass yields. Limonene exhibited both higher number concentrations and greater mass concentrations at higher [NO2]. SOA from each experiment was collected and analyzed by HPLC-ESI-MS, enabling comparisons between product distributions for each system. In general, the systems influenced by NO3 oxidation contained more high molecular weight products (MW > 400 amu), suggesting the importance of oligomerization mechanisms in NO3-initiated SOA formation. α-Pinene, which showed anomalously low aerosol mass yields in the presence of NO2, showed no increase in these oligomer peaks, suggesting that lack of oligomer formation is a likely cause of α-pinene's near 0 % yields with NO3. Through direct comparisons of mixed-oxidant systems, this work suggests that NO3 is likely to dominate nighttime oxidation pathways in most regions with both biogenic and anthropogenic influences. Therefore, accurately constraining SOA yields from NO3 oxidation, which vary substantially with the volatile organic compound precursor, is essential in predicting nighttime aerosol production.

Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses.

Forkhead-associated (FHA) domain is the only signaling domain that recognizes phosphothreonine (pThr) specifically. TRAF-interacting protein with an FHA domain (TIFA) was shown to be involved in immune responses by binding with TRAF2 and TRAF6. We recently reported that TIFA is a dimer in solution and that, upon stimulation by TNF-α, TIFA is phosphorylated at Thr9, which triggers TIFA oligomerization via pThr9-FHA domain binding and activates nuclear factor κB (NF-κB). However, the structural mechanism for the functionally important TIFA oligomerization remains to be established. While FHA domain-pThr binding is known to mediate protein dimerization, its role in oligomerization has not been demonstrated at the structural level. Here we report the crystal structures of TIFA (residues 1-150, with the unstructured C-terminal tail truncated) and its complex with the N-terminal pThr9 peptide (residues 1-15), which show unique features in the FHA structure (intrinsic dimer and extra β-strand) and in its interaction with the pThr peptide (with residues preceding rather than following pThr). These structural features support previous and additional functional analyses. Furthermore, the structure of the complex suggests that the pThr9-FHA domain interaction can occur only between different sets of dimers rather than between the two protomers within a dimer, providing the structural mechanism for TIFA oligomerization. Our results uncover the mechanism of FHA domain-mediated oligomerization in a key step of immune responses and expand the paradigm of FHA domain structure and function.

Assembling the puzzle: Oligomerization of α-pore forming proteins in membranes

Pore forming proteins (PFPs) share the ability of creating pores that allow the passage of ions, proteins or other constituents through a wide variety of target membranes, ranging from bacteria to humans. They often cause cell death, as pore formation disrupts the membrane permeability barrier required for maintaining cell homeostasis. The organization into supramolecular complexes or oligomers that pierce the membrane is a common feature of PFPs. However, the molecular pathway of self-assembly and pore opening remains unclear. Here, we review the most recent discoveries in the mechanism of membrane oligomerization and pore formation of a subset of PFPs, the α-PFPs, whose pore-forming domains are formed by helical segments. Only now we are starting to grasp the molecular details of their function, mainly thanks to the introduction of single molecule microscopy and nanoscopy techniques. This article is part of a Special Issue entitled: Pore-forming toxins edited by Mauro Dalla Serra and Franco Gambale.

Protein Cross-Linking and Oligomerization through Dityrosine Formation upon Exposure to Ozone.

Air pollution is a potential driver for the increasing prevalence of allergic disease, and post-translational modification by air pollutants can enhance the allergenic potential of proteins. Here, the kinetics and mechanism of protein oligomerization upon ozone (O3) exposure were studied in coated-wall flow tube experiments at environmentally relevant O3 concentrations, relative humidities and protein phase states (amorphous solid, semisolid, and liquid). We observed the formation of protein dimers, trimers, and higher oligomers, and attribute the cross-linking to the formation of covalent intermolecular dityrosine species. The oligomerization proceeds fast on the surface of protein films. In the bulk material, reaction rates are limited by diffusion depending on phase state and humidity. From the experimental data, we derive a chemical mechanism and rate equations for a kinetic multilayer model of surface and bulk reaction enabling the prediction of oligomer formation. Increasing levels of tropospheric O3 in the Anthropocene may promote the formation of protein oligomers with enhanced allergenicity and may thus contribute to the increasing prevalence of allergies.

Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD1(2SH)). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD1(2SH) has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization.

Functional characterization of Val60, a key residue involved in the membrane-oligomerization of fragaceatoxin C, an actinoporin from Actinia fragacea

Actinoporins are pore-forming toxins produced by different sea anemones that self-assemble within the membranes of their target cells and compromise their function as a permeability barrier. The recently published three-dimensional structures of two oligomeric complexes formed by fragaceatoxin C point to Val60 as a key residue involved in the oligomerization of the functional pore.To gain insight into the mechanism of toxin oligomerization, different point mutations have been introduced at this position. Functional characterization of the muteins suggests that Val60 represents a hot-spot where the introduction of mutations hinders protein assembly and reduces the overall affinity for membranes.

Crystal structure of Alanine‐Copper(II) complex to understand the mechanism of salt induced prebiotic oligomerization of amino acids

Oligomerization of amino acid monomers is the vital step in the formation of longer peptides and functional proteins. In spite of continuing efforts towards solving the puzzle of origin of life, the mystery of chemical evolution remains unsolved. Out of various pathways proposed for the formation of peptides under prebiotic conditions, salt induced peptides synthesis presents the most plausible scenario. In attempts to study mechanism of prebiotic oligomerization of amino acid on primitive earth the current study was aimed to determine the crystal structure of intermediate copper amino acid complex and its supra‐molecular assembly. The Structure of the copper alanine complex obtained from SIPF was studied by x‐ray crystallography. The self‐assembling properties of complex into supra‐molecular nanostructures were studied using Field‐emission electron microscopy (FE‐SEM). Results showed the occurrence of racemization of amino acids. This is the first structural study for copper alanine complex formed from prebiotic peptide synthesis pathway. The aggregational properties of intermediate complex showed the formation of rod like crystals and nanospheres. The findings from our study showed the possible mechanism of prebiotic oligomerization of amino acids on the primitive earth towards formation of longer peptides and functional proteins.