Spatial extent of charge repulsion regulates assembly pathways for lysozyme amyloid fibrils

Formation of large protein fibrils with a characteristic cross β-sheet architecture is the key indicator for a wide variety of systemic and neurodegenerative amyloid diseases. Recent experiments have strongly implicated oligomeric intermediates, transiently formed during fibril assembly, as critical contributors to cellular toxicity in amyloid diseases. At the same time, amyloid fibril assembly can proceed along different assembly pathways that might or might not involve such oligomeric intermediates. Elucidating the mechanisms that determine whether fibril formation proceeds along non-oligomeric or oligomeric pathways, therefore, is important not just for understanding amyloid fibril assembly at the molecular level but also for developing new targets for intervening with fibril formation. We have investigated fibril formation by hen egg white lysozyme, an enzyme for which human variants underlie non-neuropathic amyloidosis. Using a combination of static and dynamic light scattering, atomic force microscopy and circular dichroism, we find that amyloidogenic lysozyme monomers switch between three different assembly pathways: from monomeric to oligomeric fibril assembly and, eventually, disordered precipitation as the ionic strength of the solution increases. Fibril assembly only occurred under conditions of net repulsion among the amyloidogenic monomers while net attraction caused precipitation. The transition from monomeric to oligomeric fibril assembly, in turn, occurred as salt-mediated charge screening reduced repulsion among individual charged residues on the same monomer. We suggest a model of amyloid fibril formation in which repulsive charge interactions are a prerequisite for ordered fibril assembly. Furthermore, the spatial extent of non-specific charge screening selects between monomeric and oligomeric assembly pathways by affecting which subset of denatured states can form suitable intermolecular bonds and by altering the energetic and entropic requirements for the initial intermediates emerging along the monomeric vs. oligomeric assembly path.     

Spontaneous Structural Changes in Actin Regulate G-F Transformation

Transformations between G- (monomeric) and F-actin (polymeric) are important in cellular behaviors such as migration, cytokinesis, and morphing. In order to understand these transitions, we combined single-molecule Förster resonance energy transfer with total internal reflection fluorescence microscopy to examine conformational changes of individual actin protomers. We found that the protomers can take different conformational states and that the transition interval is in the range of hundreds of seconds. The distribution of these states was dependent on the environment, suggesting that actin undergoes spontaneous structural changes that accommodate itself to polymerization.     

Cell responses regulated by early reorganization of actin cytoskeleton

Microfilaments exist in a dynamic equilibrium between monomeric and polymerized actin and the ratio of monomers to polymeric forms is influenced by a variety of extracellular stimuli. The polymerization, depolymerization and redistribution of actin filaments are modulated by several actin-binding proteins, which are regulated by upstream signalling molecules. Actin cytoskeleton is involved in diverse cellular functions including migration, ion channels activity, secretion, apoptosis and cell survival. In this review we have outlined the role of actin dynamics in representative cell functions induced by the early response to extracellular stimuli.     

Probing actin polymerization by intermolecular cross-linking

We have used N,N'-1,4-phenylenebismaleimide, a bifunctional sulfhydryl cross-linking reagent, to probe the oligomeric state of actin during the early stages of its polymerization into filaments. We document that one of the first steps in the polymerization of globular monomeric actin (G-actin) under a wide variety of ionic conditions is the dimerization of a significant fraction of the G-actin monomer pool. As polymerization proceeds, the yield of this initial dimer ("lower" dimer with an apparent molecular mass of 86 kD by SDS-PAGE [LD]) is attenuated, while an actin filament dimer ("upper" dimer with an apparent molecular mass of 115 kD by SDS-PAGE [UD] as characterized [Elzinga, M., and J. J. Phelan. 1984. Proc. Natl. Acad. Sci. USA. 81:6599-6602]) is formed. This shift from LD to UD occurs concomitant with formation of filaments as assayed by N-(1-pyrenyl)iodoacetamide fluorescence enhancement and electron microscopy. Isolated cross-linked LD does not form filaments, while isolated cross-linked UD will assemble into filaments indistinguishable from those polymerized from unmodified G-actin under typical filament-forming conditions. The presence of cross-linked LD does not effect the kinetics of polymerization of actin monomer, whereas cross-linked UD shortens the "lag phase" of the polymerization reaction in a concentration-dependent fashion. Several converging lines of evidence suggest that, although accounting for a significant oligomeric species formed during early polymerization, the LD is incompatible with the helical symmetry defining the mature actin filament; however, it could represent the interfilament dimer found in paracrystalline arrays or filament bundles. Furthermore, the LD is compatible with the unit cell structure and symmetry common to various types of crystalline actin arrays (Aebi, U., W. E. Fowler, G. Isenberg, T. D. Pollard, and P. R. Smith. 1981. J. Cell Biol. 91:340-351) and might represent the major structural state in which a mutant beta-actin (Leavitt, J., G. Bushar, T. Kakunaga, H. Hamada, T. Hirakawa, D. Goldman, and C. Merril. 1982. Cell. 28:259-268) is arrested under polymerizing conditions.     

Actin localization in nuclei of two-cell mouse embryos

In this study, preimplantation mouse embryos were used as a new model for the study of actin distribution in nuclei and the identification of functional forms of nuclear actin. The combination of the direct detection of actin by fluorescent-conjugated phalloidin and DNase I with indirect immunofluorecence was applied as an integrated approach to studying the localization of actin in nuclei of two-cell mouse embryos. Aggregates of monomeric actin and two oligomeric forms of actin were revealed in nuclei. Each of these forms demonstrated their own pattern of distribution. Oligomeric actin recognized by antibodies to the actin C-terminal domain was associated with condensed chromatin, as well as with metaphase chromosomes and chromatin of the second polar body. Monomeric actin and another oligomeric form recognized by antibodies to actin N-terminal domain were revealed in the area of dispersed chromatin localization.     

Expression of a nonpolymerizable actin mutant in Sf9 cells

We have succeeded in expressing actin in the baculovirus/Sf9 cell system in high yield. The wild-type (WT) actin is functionally indistinguishable from tissue-purified actin in its ability to activate ATPase activity and to support movement in an in vitro motility assay. Having achieved this feat, we used a mutational strategy to express a monomeric actin that is incapable of polymerization. Native actin requires actin binding proteins or chemical modification to maintain it in a monomeric state. The mutant actin sediments in the analytical ultracentrifuge as a homogeneous monomeric species of 3.2 S in 100 mM KCl and 2 mM MgCl(2), conditions that cause WT actin to polymerize. The two point mutations that render actin nonpolymerizable are in subdomain 4 (A204E/P243K; "AP-actin"), distant from the myosin binding site. AP-actin binds to skeletal myosin subfragment 1 (S1) and forms a homogeneous complex as demonstrated by analytical ultracentrifugation. The ATPase activity of a cross-linked AP-actin.S1 complex is higher than that of S1 alone, although less than that supported by filamentous actin (F-actin). AP-Actin is an excellent candidate for structural studies of complexes of actin with motor proteins and other actin-binding proteins.     

Nucleotide effects on the structure and dynamics of actin

Adenosine 5'-triphosphate or ATP is the primary energy source within the cell, releasing its energy via hydrolysis into adenosine 5'-diphosphate or ADP. Actin is an important ATPase involved in many aspects of cellular function, and the binding and hydrolysis of ATP regulates its polymerization into actin filaments as well as its interaction with a host of actin-associated proteins. Here we study the dynamics of monomeric actin in ATP, ADP-Pi, and ADP states via molecular dynamics simulations. As observed in some crystal structures we see that the DNase-I loop is an alpha-helix in the ADP state but forms an unstructured coil domain in the ADP-Pi and ATP states. We also find that this secondary structure change is reversible, and by mimicking nucleotide exchange we can observe the transition between the helical and coil states. Apart from the DNase-I loop, we also see several key structural differences in the nucleotide binding cleft as well as in the hydrophobic cleft between subdomains 1 and 3 where WH2-containing proteins have been shown to interact. These differences provide a structural basis for understanding the observed differences between the various nucleotide states of actin and provide some insight into how ATP regulates the interaction of actin with itself and other proteins.     

Actin in B16 melanoma cells of differing metastatic potential : Effects of trypsin and serum

Actin is present in cells in monomeric and polymeric (filamentous) forms. Filamentous actin is distributed in Triton-soluble (cytosolic) and Triton-insoluble (cytoskeletal core) fractions. We have used the DNase 1 inhibition assay and immunofluorescence to investigate the distribution of actin in monomeric and polymeric forms in cloned B16 murine melanoma cell lines of low and high metastatic capacity. The protease trypsin caused rounding up and detachment of both cell lines within 5 min. This was associated with almost complete depolymerization of cytosolic actin filaments but the Triton-insoluble cytoskeleton was not quantitatively affected by trypsin treatment. There were quantitative differences between the clones in their response to incubation in the presence or absence of 10% serum. The highly metastatic cell line contained 35% more actin when incubated in the presence of 10% serum, almost completely distributed to the Triton-insoluble cytoskeleton, an effect not seen in the low metastatic cells.     

State of protein B23/nucleophosmin in brain cells

Protein B23/nucleophosmin is a polyfunctional protein existing in cells in numerous structural forms. In this work, for the immunochemical analysis of nucleophosmin we used the antibodies specific to different forms of nucleophosmin, namely, antibodies selectively revealing monomers of all the known forms of this protein and antibodies specific only to isoform B23.1. Homogenates of different rat tissues such as the brain, liver, kidney, lung and heart were used, as well as nuclei from liver and brain cells. For the first time, we show that the structural state of nucleophosmin in brain differs from its state in other tissues, including the liver that is enriched with nucleophosmin. It was revealed that on immunoblots of brain homogenates not only monomeric form of nucleophosmin but also unique SDS-resistant oligomeric forms were detected in the SDS-PAGE. Analysis of nucleophosmin in the cerebellum, cortex, amygdala, brainstem, and hippocampus showed that most enriched with nucleophosmin were hippocampus and cerebellum; on their immunoblots SDS-resistant oligomeric forms of nucleophosmin dominated. Using immunochemical analysis of the protein in primary cultures of cerebellum glial cells and neurons, significant structural differences of nucleophosmin in proliferating glial cells and non-proliferating neurons were revealed for the first time. It was found also that the nucleophosmin content in glial cells is much higher than in neurons and that the main forms of protein B23 in glial cells on immunoblots are the SDS-resistant oligomers, while a monomeric form was present in much smaller quantities. In contrast to glial cells, neurons did not contain such oligomers. In neurons, only trace amounts of a monomeric form of nucleophosmin were found, which were undetectable by the antibodies specific to isoform B23.1.     

pH control of actin polymerization by cofilin

Cofilin, a 21,000 molecular weight actin-regulatory protein (Nishida, E., Maekawa, S., and Sakai, H. (1984) Biochemistry 23, 5307-5313), was here shown to be capable of reversibly controlling actin polymerization and depolymerization in a pH-sensitive manner. When cofilin was reacted with F-actin at different pH, the depolymerized actin concentration (= monomeric actin concentration) was higher at elevated pH. At pH less than 7.3, the monomeric actin concentrations did not exceed approximately 1 microM even in the presence of excess amounts of cofilin, whereas at pH greater than 7.3 it increased in proportion to the concentration of cofilin added, and complete depolymerization of F-actin occurred by the addition of an excess amount of cofilin. Moreover, in the presence of cofilin, rapid interconversion of monomeric and polymeric forms of actin can be induced by simply changing the pH of the medium. Thus, this study provides a new possible mechanism regulating actin polymerization, pH control.     

Discoidin domain receptors: Micro insights into macro assemblies

Assembly of cell-surface receptors into specific oligomeric states and/or clusters before and after ligand binding is an important feature governing their biological function. Receptor oligomerization can be mediated by specific domains of the receptor, ligand binding, configurational changes or other interacting molecules. In this review we summarize our understanding of the oligomeric state of discoidin domain receptors (DDR1 and DDR2), which belong to the receptor tyrosine kinase family (RTK). DDRs form an interesting system from an oligomerization perspective as their ligand collagen(s) can also undergo supramolecular assembly to form fibrils. Even though DDR1 and DDR2 differ in the domains responsible to form ligand-free dimers they share similarities in binding to soluble, monomeric collagen. However, only DDR1b forms globular clusters in response to monomeric collagen and not DDR2. Interestingly, both DDR1 and DDR2 are assembled into linear clusters by the collagen fibril. Formation of these clusters is important for receptor phosphorylation and is mediated in part by other membrane components. We summarize how the oligomeric status of DDRs shares similarities with other members of the RTK family and with collagen receptors. Unraveling the multiple macro-molecular configurations adopted by this receptor-ligand pair can provide novel insights into the intricacies of cell-matrix interactions.     

Study of the quaternary structure of rat 1-Cys peroxiredoxin

Peroxiredoxins (Prx) are a family of antioxidant proteins with peroxidase activity. The ability of 1-Cys Prx to self-associate was studied with the use of native PAGE and Western blotting. Two protein bands corresponding to monomeric and dimeric forms were detected in the preparation of the recombinant 1-Cys Prx subjected to native PAGE, with dimers being more abundant. The third band corresponding to the oligomeric form was detected after incubation of the recombinant 1-Cys Prx with DTT, although monomers and dimers were also observed. These results indicate that monomeric, dimeric, and oligomeric states of the protein are likely to be interchangeable. Native PAGE in combination with Western blot analysis revealed that self-association of 1-Cys Prx also occurred at physiologically relevant concentrations in vivo. The native 1-Cys Prx existed in the monomeric and dimeric forms in rat olfactory epithelium, with monomers being more common. The structural sensitivity of the recombinant 1-Cys Prx to imidazole was shown.     

Comparison between actin filament models: coarse-graining reveals essential differences

The interconversion of actin between monomeric and polymeric forms is a fundamental process in cell biology that is incompletely understood, in part because there is no high-resolution structure for filamentous actin. Several models have been proposed recently; identifying structural and dynamic differences between them is an essential step toward understanding actin dynamics. We compare three of these models, using coarse-grained analysis of molecular dynamics simulations to analyze the differences between them and evaluate their relative stability. Based on this analysis, we identify key motions that may be associated with polymerization, including a potential energetic barrier in the process. We also find that actin subunits are polymorphic; during simulations they assume a range of configurations remarkably similar to those seen in recent cryoEM images.     

Early events in the fibrillation of monomeric insulin

Insulin has a largely alpha-helical structure and exists as a mixture of hexameric, dimeric, and monomeric states in solution, depending on the conditions: the protein is monomeric in 20% acetic acid. Insulin forms amyloid-like fibrils under a variety of conditions, especially at low pH. In this study we investigated the fibrillation of monomeric human insulin by monitoring changes in CD, attenuated total reflectance-Fourier transform infrared spectroscopy, 8-anilinonaphthalenesulfonic acid fluorescence, thioflavin T fluorescence, dynamic light scattering, and H/D exchange during the initial stages of the fibrillation process to provide insight into early events involving the monomer. The results demonstrate the existence of structural changes occurring before the onset of fibril formation, which are detectable by multiple probes. The data indicate at least two major populations of oligomeric intermediates between the native monomer and fibrils. Both have significantly non-native conformations, and indicate that fibrillation occurs from a beta-rich structure significantly distinct from the native fold.     

Activity of rheumatoid factors of different molecular sizes: comparison of autologous monomeric and polymeric monoclonal IgA rheumatoid factors

Differences in rheumatoid factor (RF) activity among the molecular species of IgA were investigated with the use of monomeric and polymeric monoclonal IgA RF paraprotein from the serum of a patient (PS) with idiopathic hyperviscosity syndrome. After fractionation by gel chromatography in acidic buffer, RF activity as determined by latex fixation and solid-phase radioimmunoassay (RIA) specific for IgA RF was confined to the high m.w. (greater than 7S) fractions. However, after adsorption into polystyrene wells, fractions containing monomeric (7S) IgA, as well as those containing polymeric IgA, bound 125I-labeled heat-aggregated human IgG. These observations were confirmed after further purification of the IgA fractions by passage through a protein A-Sepharose CL-4B column followed by precipitation of the IgA proteins with ammonium sulfate at 50% saturation. After "cross-linkage" by a hybridoma anti-human alpha-chain antibody, the activity of the monomeric IgA preparation in the IgA RF RIA approached that of the polymeric IgA preparation. Gel filtration studies verified that this activity was not due to contamination by polymeric IgA RF. Further, classic RF specificity was confirmed for both the monomeric and polymeric IgA RF by reaction with human Fc-coated but not Fab-coated wells. A control monomeric IgA myeloma protein and normal serum IgA did not react in the RF RIA when analyzed in the presence or absence of the hybridoma anti-alpha-chain antibody. Moreover, the activity of the polymeric IgA RF preparation from patient PS in the RIA was minimally influenced by the hybridoma antibody. These results indicate that IgA RF can coexist in both polymeric and monomeric forms, demonstrate that monomeric IgA RF may escape detection by previously described RIA techniques, and suggest an approach for its detection.     

Structural variations in actins. Biochemical and immunological tools for probing the structure of rabbit skeletal-muscle and bovine aortic actins.

Structural differences between skeletal-muscle and aortic actins were studied by using biochemical and immunological approaches. By using proteinase digestion we found that three regions of actin show structural differences: (a) in the C-terminal part, (b) the region around residue 227 and (c) the region around residue 167. By using antibodies specific to particular actin conformations we can discriminate between monomeric and filamentous forms of the two actins. Our results show that the minor sequence variations of the N- and C-terminal regions induce structural change in these regions, but also some long-range structural variations in other regions.     

Interaction of NAD-kinase with glutamate dehydrogenase

The formation of a NAD kinase-glutamate dehydrogenase complex was studied, using three independent methods. It was found that the polymeric form of glutamate dehydrogenase is involved in the formation of a complex with NAD kinase. Both the oligomeric and monomeric (subunit) forms of NAD kinase were shown to possess the ability to form complexes with glutamate dehydrogenase.     

States and transitions during forced unfolding of a single spectrin repeat

Spectrin is a vital and abundant protein of the cytoskeleton. It has an elongated structure that is made by a chain of so-called spectrin repeats. Each repeat contains three antiparallel alpha-helices that form a coiled-coil structure. Spectrin forms an oligomeric structure that is able to cross-link actin filaments. In red cells, the spectrin/actin meshwork underlying cell membrane is thought to be responsible for special elastic properties of the cell. In order to determine mechanical unfolding properties of the spectrin repeat, we have used single molecule force spectroscopy to study the states of unfolding of an engineered polymeric protein consisting of identical spectrin domains. We demonstrate that the unfolding of spectrin domains can occur in a stepwise fashion during stretching. The force-extension patterns exhibit features that are compatible with the existence of at least one intermediate between the folded and the completely unfolded conformation. Only those polypeptides that still contain multiple intact repeats display intermediates, indicating a stabilisation effect. Precise force spectroscopy measurements on single molecules using engineered protein constructs reveal states and transitions during the mechanical unfolding of spectrin. Single molecule force spectroscopy appears to open a new window for the analysis of transition probabilities between different conformational states.