Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 573
Filter
1.
J Mol Biol ; 435(22): 168285, 2023 11 15.
Article in English | MEDLINE | ID: mdl-37741548

ABSTRACT

Amyloid formation due to protein misfolding has gained significant attention due to its association with neurodegenerative diseases. α-Synuclein (α-syn) is one such protein that undergoes a profound conformational switch to form higher order cross-ß-sheet structures, resulting in amyloid formation, which is linked to the pathophysiology of Parkinson's disease (PD). The present status of research on α-syn aggregation and PD reveals that the disease progression may be linked with many other diseases, such as kidney-related disorders. Unraveling the link between PD and non-neurological diseases may help in early detection and a better understanding of PD progression. Herein, we investigated the modulation of α-syn in the presence of ß2-microglobulin (ß2m), a structural protein associated with dialysis-related amyloidosis. We took a multi-disciplinary approach to establish that ß2m mitigates amyloid formation by α-syn. Our fluorescence, microscopy and toxicity data demonstrated that sub-stoichiometric ratio of ß2m drives α-syn into off-pathway non-toxic aggregates incompetent of transforming into amyloids. Using AlphaFold2 and all-atom MD simulation, we showed that the ß-strand segments (ß1 and ß2) of α-synuclein, which frequently engage in interactions within amyloid fibrils, interact with the last ß-strand at the C-terminal of ß2m. The outcome of this study will unravel the yet unknown potential linkage of PD with kidney-related disorders. Insights from the cross-talk between two amyloidogenic proteins will lead to early diagnosis and new therapeutic approaches for treating Parkinson's disease. Finally, disruption of the nucleation process of α-syn amyloids by targeting the ß1-ß2 region will constitute a potential therapeutic approach for inhibiting amyloid formation.


Subject(s)
Amyloid , Parkinson Disease , Protein Aggregates , alpha-Synuclein , beta 2-Microglobulin , Humans , alpha-Synuclein/chemistry , Amyloid/chemistry , Amyloidogenic Proteins , Parkinson Disease/metabolism , Renal Dialysis/adverse effects , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/metabolism , Molecular Docking Simulation , Models, Molecular , Protein Conformation
2.
J Phys Chem B ; 127(31): 6887-6895, 2023 08 10.
Article in English | MEDLINE | ID: mdl-37527428

ABSTRACT

Conformational dynamics in proteins can give rise to aggregation prone states during folding, and these kinetically stable states could form oligomers and aggregates. In this study, we investigate the intermediate states and near-folded states of ß2-microglobulin and their physico-chemical properties using molecular dynamics and Markov state modeling. Analysis of hundreds of microseconds simulation show the importance of the edge strands in the misfolded states that give rise to a high exposure of hydrophobic residues in the core of the protein that could initiate oligomerization and aggregate formation. Our study sheds light on the first step of aggregation of ß2m monomers and gave a better picture of the landscape of protein misfolding and aggregation.


Subject(s)
Molecular Dynamics Simulation , beta 2-Microglobulin , beta 2-Microglobulin/chemistry , Molecular Conformation , Amyloid/chemistry , Protein Folding
3.
Protein Sci ; 32(1): e4487, 2023 01.
Article in English | MEDLINE | ID: mdl-36321362

ABSTRACT

ß2 -Microglobulin (ß2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured ß2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized ß2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced ß2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized ß2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured ß2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.


Subject(s)
Amyloid , beta 2-Microglobulin , Hydrogen-Ion Concentration , Amyloid/chemistry , beta 2-Microglobulin/chemistry , Disulfides/chemistry
4.
J Biol Chem ; 298(12): 102659, 2022 12.
Article in English | MEDLINE | ID: mdl-36328246

ABSTRACT

Self-association of WT ß2-microglobulin (WT-ß2m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-ß2m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-ß2m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-ß2m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-ß2m. We show that the crosslinked D76N-ß2m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-ß2m and are unable to assemble into amyloid. Instead, the crosslinked D76N-ß2m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-ß2m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.


Subject(s)
Amyloidosis , beta 2-Microglobulin , Humans , beta 2-Microglobulin/chemistry , Amyloid/chemistry , Amyloidogenic Proteins/genetics , Amino Acid Substitution , Amyloidosis/genetics , Biophysical Phenomena , Polymers
5.
Molecules ; 27(14)2022 Jul 19.
Article in English | MEDLINE | ID: mdl-35889461

ABSTRACT

The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute's concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.


Subject(s)
Amyloid , Amyloidosis , Amyloid/chemistry , Amyloidosis/metabolism , Humans , Solutions , Thermodynamics , beta 2-Microglobulin/chemistry
6.
Proc Natl Acad Sci U S A ; 119(22): e2200468119, 2022 05 31.
Article in English | MEDLINE | ID: mdl-35613051

ABSTRACT

Aggregation of initially stably structured proteins is involved in more than 20 human amyloid diseases. Despite intense research, however, how this class of proteins assembles into amyloid fibrils remains poorly understood, principally because of the complex effects of amino acid substitutions on protein stability, solubility, and aggregation propensity. We address this question using ß2-microglobulin (ß2m) as a model system, focusing on D76N-ß2m that is involved in hereditary amyloidosis. This amino acid substitution causes the aggregation-resilient wild-type protein to become highly aggregation prone in vitro, although the mechanism by which this occurs remained elusive. Here, we identify the residues key to protecting ß2m from aggregation by coupling aggregation with antibiotic resistance in E. coli using a tripartite ß-lactamase assay (TPBLA). By performing saturation mutagenesis at three different sites (D53X-, D76X-, and D98X-ß2m) we show that residue 76 has a unique ability to drive ß2m aggregation in vivo and in vitro. Using a randomly mutated D76N-ß2m variant library, we show that all of the mutations found to improve protein behavior involve residues in a single aggregation-prone region (APR) (residues 60 to 66). Surprisingly, no correlation was found between protein stability and protein aggregation rate or yield, with several mutations in the APR decreasing aggregation without affecting stability. Together, the results demonstrate the power of the TPBLA to develop proteins that are resilient to aggregation and suggest a model for D76N-ß2m aggregation involving the formation of long-range couplings between the APR and Asn76 in a nonnative state.


Subject(s)
Amyloidosis , Protein Aggregation, Pathological , beta 2-Microglobulin , Amino Acid Substitution , Amyloidogenic Proteins/genetics , Amyloidosis/genetics , Enzyme Assays , Escherichia coli , Humans , Point Mutation , Protein Aggregation, Pathological/genetics , Protein Folding , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/genetics , beta-Lactamases
7.
Acta Biochim Biophys Sin (Shanghai) ; 54(2): 187-198, 2022 01 25.
Article in English | MEDLINE | ID: mdl-35130623

ABSTRACT

The ΔN6 truncation is the main posttranslational modification of ß-microglobulin (ßM) found in dialysis-related amyloid. Investigation of the interaction of wild-type (WT) ßM with N-terminally truncated variants is therefore of medical relevance. However, it is unclear which residues among the six residues at the N-terminus are crucial to the interactions and the modulation of amyloid fibril propagation of ßM. We herein analyzed homo- and heterotypic seeding of amyloid fibrils of WT human ßM and its N-terminally-truncated variants ΔN1 to ΔN6, lacking up to six residues at the N-terminus. At acidic pH 2.5, we produced amyloid fibrils from recombinant, WT ßM and its six truncated variants, and found that ΔN6 ßM fibrils exhibit a significantly lower conformational stability than WT ßM fibrils. Importantly, under more physiological conditions (pH 6.2), we assembled amyloid fibrils only from recombinant, ΔN4, ΔN5, and ΔN6 ßM but not from WT ßM and its three truncated variants ΔN1 to ΔN3. Notably, the removal of the six, five or four residues at the N-terminus leads to enhanced fibril formation, and homo- and heterotypic seeding of ΔN6 fibrils strongly promotes amyloid fibril formation of WT ßM and its six truncated variants, including at more physiological pH 6.2. Collectively, these results demonstrated that the residues 4 to 6 at the N-terminus particularly modulate amyloid fibril propagation of ßM and the interactions of WT ßM with N-terminally truncated variants, potentially indicating the direct relevance to the involvement of the protein's aggregation in dialysis-related amyloidosis.


Subject(s)
Amyloid , beta 2-Microglobulin , Amyloid/chemistry , Amyloid/genetics , Humans , Hydrogen-Ion Concentration , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/genetics
8.
Phys Chem Chem Phys ; 24(3): 1630-1637, 2022 Jan 19.
Article in English | MEDLINE | ID: mdl-34951613

ABSTRACT

The nature of the nanoparticle-protein corona is emerging as a key aspect in determining the impact of nanomaterials on proteins and in general on the biological response. We previously demonstrated that citrate-stabilized gold nanoparticles (Cit-AuNPs) interact with ß2-microglobulin (ß2m) preserving the protein native structure. Moreover, Cit-AuNPs are able to hinder in vitro fibrillogenesis of a ß2m pathologic variant, namely D76N, by reducing the oligomeric association of the protein in solution. Here, we clarify the characteristics of the interaction between ß2m and Cit-AuNPs by means of different techniques, i.e. surface enhanced Raman spectroscopy, NMR and quartz crystal microbalance with dissipation monitoring. All the results obtained clearly show that by simply changing the ionic strength of the medium it is possible to switch from a labile and transient nature of the protein-NP adduct featuring the so-called soft corona, to a more "hard" interaction with a layer of proteins having a longer residence time on the NP surface. This confirms that the interaction between ß2m and Cit-AuNPs is dominated by electrostatic forces which can be tuned by modifying the ionic strength.


Subject(s)
Metal Nanoparticles/chemistry , Protein Corona/chemistry , beta 2-Microglobulin/chemistry , Citrates/chemistry , Gold/chemistry , Mutation , Osmolar Concentration , Static Electricity , beta 2-Microglobulin/genetics
9.
J Biol Chem ; 297(5): 101286, 2021 11.
Article in English | MEDLINE | ID: mdl-34626645

ABSTRACT

Amyloid fibrils, crystal-like fibrillar aggregates of proteins associated with various amyloidoses, have the potential to propagate via a prion-like mechanism. Among known methodologies to dissolve preformed amyloid fibrils, acid treatment has been used with the expectation that the acids will degrade amyloid fibrils similar to acid inactivation of protein functions. Contrary to our expectation, treatment with strong acids, such as HCl or H2SO4, of ß2-microglobulin (ß2m) or insulin actually promoted amyloid fibril formation, proportionally to the concentration of acid used. A similar promotion was observed at pH 2.0 upon the addition of salts, such as NaCl or Na2SO4. Although trichloroacetic acid, another strong acid, promoted amyloid fibril formation of ß2m, formic acid, a weak acid, did not, suggesting the dominant role of anions in promoting fibril formation of this protein. Comparison of the effects of acids and salts confirmed the critical role of anions, indicating that strong acids likely induce amyloid fibril formation via an anion-binding mechanism. The results suggest that although the addition of strong acids decreases pH, it is not useful for degrading amyloid fibrils, but rather induces or stabilizes amyloid fibrils via an anion-binding mechanism.


Subject(s)
Amyloid/chemistry , Protein Aggregates , beta 2-Microglobulin/chemistry , Anions/chemistry , Circular Dichroism , Humans , Hydrogen-Ion Concentration , Sodium Chloride/chemistry
10.
Int J Mol Sci ; 22(12)2021 Jun 13.
Article in English | MEDLINE | ID: mdl-34199259

ABSTRACT

Beta2-microglobulin (B2M) a key component of major histocompatibility complex class I molecules, which aid cytotoxic T-lymphocyte (CTL) immune response. However, the majority of studies of B2M have focused only on amyloid fibrils in pathogenesis to the neglect of its role of antimicrobial activity. Indeed, B2M also plays an important role in innate defense and does not only function as an adjuvant for CTL response. A previous study discovered that human aggregated B2M binds the surface protein structure in Streptococci, and a similar study revealed that sB2M-9, derived from native B2M, functions as an antibacterial chemokine that binds Staphylococcus aureus. An investigation of sB2M-9 exhibiting an early lymphocyte recruitment in the human respiratory epithelium with bacterial challenge may uncover previously unrecognized aspects of B2M in the body's innate defense against Mycobactrium tuberculosis. B2M possesses antimicrobial activity that operates primarily under pH-dependent acidic conditions at which B2M and fragmented B2M may become a nucleus seed that triggers self-aggregation into distinct states, such as oligomers and amyloid fibrils. Modified B2M can act as an antimicrobial peptide (AMP) against a wide range of microbes. Specifically, these AMPs disrupt microbe membranes, a feature similar to that of amyloid fibril mediated cytotoxicity toward eukaryotes. This study investigated two similar but nonidentical effects of B2M: the physiological role of B2M, in which it potentially acts against microbes in innate defense and the role of B2M in amyloid fibrils, in which it disrupts the membrane of pathological cells. Moreover, we explored the pH-governing antibacterial activity of B2M and acidic pH mediated B2M amyloid fibrils underlying such cytotoxicity.


Subject(s)
Amyloid/toxicity , Anti-Bacterial Agents/pharmacology , beta 2-Microglobulin/metabolism , Amino Acid Sequence , Animals , Cell Death/drug effects , Humans , Hydrogen-Ion Concentration , beta 2-Microglobulin/chemistry
11.
Phys Biol ; 18(5)2021 06 30.
Article in English | MEDLINE | ID: mdl-34098544

ABSTRACT

Protein beta-2-microglobulin (ß2m) is classically considered the causative agent of dialysis related amyloidosis, a conformational disorder that affects patients undergoing long-term hemodialysis. The wild type (WT) form, the ΔN6 structural variant, and the D76N mutant have been extensively used as model systems ofß2m aggregation. In all of them, the native structure is stabilized by a disulfide bridge between the sulphur atoms of the cysteine residues 25 (at B strand) and 80 (at F strand), which has been considered fundamental inß2m fibrillogenesis. Here, we use extensive discrete molecular dynamics simulations of a full atomistic structure-based model to explore the role of this disulfide bridge as a modulator of the folding space ofß2m. In particular, by considering different models for the disulfide bridge, we explore the thermodynamics of the folding transition, and the formation of intermediate states that may have the potential to trigger the aggregation cascade. Our results show that the dissulfide bridge affects folding transition and folding thermodynamics of the considered model systems, although to different extents. In particular, when the interaction between the sulphur atoms is stabilized relative to the other intramolecular interactions, or even locked (i.e. permanently established), the WT form populates an intermediate state featuring a well preserved core and two unstructured termini, which was previously detected only for the D76N mutant. The formation of this intermediate state may have important implications in our understanding ofß2m fibrillogenesis.


Subject(s)
Cysteine/chemistry , Disulfides/chemistry , Protein Folding , beta 2-Microglobulin/chemistry , Molecular Dynamics Simulation , Thermodynamics
12.
Int J Mol Sci ; 22(9)2021 May 02.
Article in English | MEDLINE | ID: mdl-34063223

ABSTRACT

Proteolytic enzymes are known to be involved in the formation and degradation of various monomeric proteins, but the effect of proteases on the ordered protein aggregates, amyloid fibrils, which are considered to be extremely stable, remains poorly understood. In this work we study resistance to proteolytic degradation of lysozyme amyloid fibrils with two different types of morphology and beta-2-microglobulun amyloids. We showed that the proteolytic enzyme of the pancreas, trypsin, induced degradation of amyloid fibrils, and the mechanism of this process was qualitatively the same for all investigated amyloids. At the same time, we found a dependence of efficiency and rate of fibril degradation on the structure of the amyloid-forming protein as well as on the morphology and clustering of amyloid fibrils. It was assumed that the discovered relationship between fibrils structure and the efficiency of their degradation by trypsin can become the basis of a new express method for the analysis of amyloids polymorphism. Unexpectedly lower resistance of both types of lysozyme amyloids to trypsin exposure compared to the native monomeric protein (which is not susceptible to hydrolysis) was attributed to the higher availability of cleavage sites in studied fibrils. Another intriguing result of the work is that the cytotoxicity of amyloids treated with trypsin was not only failing to decline, but even increasing in the case of beta-2-microglobulin fibrils.


Subject(s)
Amyloid/metabolism , Trypsin/metabolism , Amyloid/chemistry , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Anilino Naphthalenesulfonates , Benzothiazoles , Fluorescent Dyes , HeLa Cells , Humans , Hydrogen-Ion Concentration , Hydrolysis , Muramidase/metabolism , Proteolysis , Trypsin/chemistry , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/metabolism
13.
J Am Soc Mass Spectrom ; 32(7): 1583-1592, 2021 Jul 07.
Article in English | MEDLINE | ID: mdl-33586970

ABSTRACT

NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein ß2-microglobulin (ß2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.


Subject(s)
Hydrogen Deuterium Exchange-Mass Spectrometry/methods , Protein Footprinting/methods , beta 2-Microglobulin/chemistry , Amino Acid Substitution , Humans , Protein Conformation , beta 2-Microglobulin/analysis , beta 2-Microglobulin/genetics , beta 2-Microglobulin/metabolism
14.
Int J Mol Sci ; 22(2)2021 Jan 15.
Article in English | MEDLINE | ID: mdl-33467468

ABSTRACT

The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (ß2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against ß2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing ß2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.


Subject(s)
Computational Biology/methods , DNA, Single-Stranded/metabolism , Peptides/metabolism , beta 2-Microglobulin/metabolism , Binding Sites/genetics , Biosensing Techniques/methods , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/genetics , Humans , Kinetics , Microscopy, Atomic Force/methods , Molecular Dynamics Simulation , Peptides/chemistry , Peptides/genetics , Protein Binding , Surface Plasmon Resonance/methods , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/genetics
15.
J Biol Chem ; 296: 100333, 2021.
Article in English | MEDLINE | ID: mdl-33508321

ABSTRACT

ß2-Microglobulin (ß2m) is the causative protein of dialysis-related amyloidosis. Its unfolding mainly proceeds along the pathway of NC →UC ⇄ UT, whereas refolding follows the UT → IT (→NT) →NC pathway, in which N, I, and U are the native, intermediate, and unfolded states, respectively, with the Pro32 peptidyl-prolyl bond in cis or trans conformation as indicated by the subscript. It is noted that the IT state is a putative amyloidogenic precursor state. Several aggregation-prone variants of ß2m have been reported to date. One of these variants is D76N ß2m, which is a naturally occurring amyloidogenic mutant. To elucidate the molecular mechanisms contributing to the enhanced amyloidogenicity of the mutant, we investigated the equilibrium and kinetic transitions of pressure-induced folding/unfolding equilibria in the wild type and D76N mutant by monitoring intrinsic tryptophan and 1-anilino-8-naphthalene sulfonate fluorescence. An analysis of kinetic data revealed that the different folding/unfolding behaviors of the wild type and D76N mutant were due to differences in the activation energy between the unfolded and the intermediate states as well as stability of the native state, leading to more rapid accumulation of IT state for D76N in the refolding process. In addition, the IT state was found to assume more hydrophobic nature. These changes induced the enhanced amyloidogenicity of the D76N mutant and the distinct pathogenic symptoms of patients. Our results suggest that the stabilization of the native state will be an effective approach for suppressing amyloid fibril formation of this mutant.


Subject(s)
Amyloidosis/genetics , Mutant Proteins/chemistry , Protein Aggregates/genetics , beta 2-Microglobulin/chemistry , Amyloidosis/metabolism , Amyloidosis/pathology , Anilino Naphthalenesulfonates/chemistry , Humans , Kinetics , Mutant Proteins/genetics , Mutant Proteins/ultrastructure , Pressure , Protein Folding , Renal Dialysis/adverse effects , Signal Transduction/genetics , Tryptophan/chemistry , beta 2-Microglobulin/genetics , beta 2-Microglobulin/ultrastructure
16.
Phys Chem Chem Phys ; 23(1): 356-367, 2021 Jan 06.
Article in English | MEDLINE | ID: mdl-33346272

ABSTRACT

The protein ß2-microglobulin (ß2-m) can aggregate in insoluble amyloid fibrils, which deposit in the skeletal muscle system of patients undergoing long-term haemodialysis. The molecular mechanisms of such amyloidogenesis are still not fully understood. A potential, although debated, triggering factor is the cis to trans isomerization of a specific proline (Pro32) in ß2-m. Here we investigate this process in the native protein and in the aggregation-prone mutant D76N by means of molecular dynamics and the enhanced sampling method metadynamics. Our simulations, including the estimation of the free energy difference between the cis and trans isomers, are in good agreement with in vitro experiments and highlight the importance of the hydrogen bond and hydrophobic interaction network around the critical Pro32 in stabilizing and de-stabilizing the two isomers.


Subject(s)
Amyloidogenic Proteins/chemistry , Proline/chemistry , beta 2-Microglobulin/chemistry , Amyloidogenic Proteins/genetics , Dipeptides/chemistry , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Molecular Dynamics Simulation , Point Mutation , Protein Conformation , Stereoisomerism , beta 2-Microglobulin/genetics
17.
Biochim Biophys Acta Proteins Proteom ; 1869(3): 140593, 2021 03.
Article in English | MEDLINE | ID: mdl-33359410

ABSTRACT

The 15N-1H heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy suffers from line-broadening effects, such as chemical exchange of labile protons with solvent, and exchange broadening for residues undergoing conformational dynamics. The amide resonance of ß2-microglobulin residue S88 is not observed in the HSQC spectrum but can be obtained through 13C-detect experiments that circumvent the problem of amide-solvent exchange broadening. Line broadening of S88 resonance beyond detection in the HSQC spectrum is not attributed to conformational exchange but rather to solvent exchange occurring on the order of ~103 s-1.


Subject(s)
Amides/chemistry , Carbon Isotopes/chemistry , Proton Magnetic Resonance Spectroscopy/methods , Solvents/chemistry , beta 2-Microglobulin/chemistry , Protein Conformation
18.
Molecules ; 25(21)2020 Nov 07.
Article in English | MEDLINE | ID: mdl-33171781

ABSTRACT

BACKGROUND: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, ß2-microglobulin (ß2m), which may be regarded as a paradigmatic system for possible therapeutic strategies. Previous evidence showed in fact that gold nanoparticles (AuNPs) are able to inhibit ß2m fibril formation in vitro. METHODS: NMR (Nuclear Magnetic Resonance) and ESR (Electron Spin Resonance) spectroscopy are employed to characterize the paramagnetic perturbation of the extrinsic nitroxide probe Tempol on ß2m in the absence and presence of AuNPs to determine the surface accessibility properties and the occurrence of chemical or conformational exchange, based on measurements conducted under magnetization equilibrium and non-equilibrium conditions. RESULTS: The nitroxide perturbation analysis successfully identifies the protein regions where protein-protein or protein-AuNPs interactions hinder accessibility or/and establish exchange contacts. These information give interesting clues to recognize the fibrillation interface of ß2m and hypothesize a mechanism for AuNPs fibrillogenesis inhibition. CONCLUSIONS: The presented approach can be advantageously applied to the characterization of the interface in protein-protein and protein-nanoparticles interactions.


Subject(s)
Magnetic Resonance Spectroscopy/methods , Nanoparticles/chemistry , Proteins/chemistry , beta 2-Microglobulin/chemistry , Amyloid/chemistry , Cyclic N-Oxides/pharmacology , Dimerization , Electron Spin Resonance Spectroscopy , Gold/chemistry , Metal Nanoparticles/chemistry , Models, Molecular , Protein Domains , Protein Interaction Mapping , Spectrophotometry , Spin Labels
19.
J Am Chem Soc ; 142(49): 20845-20854, 2020 12 09.
Article in English | MEDLINE | ID: mdl-33253560

ABSTRACT

Protein-protein interactions (PPIs) are involved in many of life's essential biological functions yet are also an underlying cause of several human diseases, including amyloidosis. The modulation of PPIs presents opportunities to gain mechanistic insights into amyloid assembly, particularly through the use of methods which can trap specific intermediates for detailed study. Such information can also provide a starting point for drug discovery. Here, we demonstrate that covalently tethered small molecule fragments can be used to stabilize specific oligomers during amyloid fibril formation, facilitating the structural characterization of these assembly intermediates. We exemplify the power of covalent tethering using the naturally occurring truncated variant (ΔN6) of the human protein ß2-microglobulin (ß2m), which assembles into amyloid fibrils associated with dialysis-related amyloidosis. Using this approach, we have trapped tetramers formed by ΔN6 under conditions which would normally lead to fibril formation and found that the degree of tetramer stabilization depends on the site of the covalent tether and the nature of the protein-fragment interaction. The covalent protein-ligand linkage enabled structural characterization of these trapped, off-pathway oligomers using X-ray crystallography and NMR, providing insight into why tetramer stabilization inhibits amyloid assembly. Our findings highlight the power of "post-translational chemical modification" as a tool to study biological molecular mechanisms.


Subject(s)
Amyloidogenic Proteins/chemistry , Amyloid/chemistry , Amyloid/metabolism , Amyloidogenic Proteins/metabolism , Crystallography, X-Ray , Disulfides/chemistry , Humans , Ligands , Magnetic Resonance Spectroscopy , Protein Interaction Domains and Motifs , Protein Multimerization , beta 2-Microglobulin/chemistry , beta 2-Microglobulin/metabolism
20.
Int J Mol Sci ; 21(20)2020 Oct 16.
Article in English | MEDLINE | ID: mdl-33081200

ABSTRACT

Given the ability of molecular chaperones and chaperone-like proteins to inhibit the formation of pathological amyloid fibrils, the chaperone-based therapy of amyloidosis has recently been proposed. However, since these diseases are often diagnosed at the stages when a large amount of amyloids is already accumulated in the patient's body, in this work we pay attention to the undeservedly poorly studied problem of chaperone and chaperone-like proteins' effect on mature amyloid fibrils. We showed that a heat shock protein alpha-B-crystallin, which is capable of inhibiting fibrillogenesis and is found in large quantities as a part of amyloid plaques, can induce degradation of mature amyloids by two different mechanisms. Under physiological conditions, alpha-B-crystallin induces fluffing and unweaving of amyloid fibrils, which leads to a partial decrease in their structural ordering without lowering their stability and can increase their cytotoxicity. We found a higher correlation between the rate and effectiveness of amyloids degradation with the size of fibrils clusters rather than with amino acid sequence of amyloidogenic protein. Some external effects (such as an increase in medium acidity) can lead to a change in the mechanism of fibrils degradation induced by alpha-B-crystallin: amyloid fibers are fragmented without changing their secondary structure and properties. According to recent data, fibrils cutting can lead to the generation of seeds for new bona fide amyloid fibrils and accelerate the accumulation of amyloids, as well as enhance the ability of fibrils to disrupt membranes and to reduce cell viability. Our results emphasize the need to test the chaperone effect not only on fibrillogenesis, but also on the mature amyloid fibrils, including stress conditions, in order to avoid undesirable disease progression during chaperone-based therapy.


Subject(s)
Amyloid/chemistry , alpha-Crystallin B Chain/chemistry , Amyloid/drug effects , HeLa Cells , Humans , Muramidase/chemistry , Protein Conformation , alpha-Crystallin B Chain/pharmacology , beta 2-Microglobulin/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL
...