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Biology subjects

Hansmann, U. H. E.

Publications and source records attributed to Hansmann, U. H. E..

At least 19 recordsLinked to original sources

Early Steps in Pathogen-induced TTR-amyloid-formation

Motivated by correlations between SARS-COV-2 infections and transthyretin (TTR) amyloidosis we use molecular dynamics simulations to study whether three protein fragments from the SARS-CoV-2 virus can initiate dissociation of the transthyretin (TTR) homotetramer as the first step on the pathway to TTR amyloidosis. We find that the peptides reduce the frequency of transient hydrogen bonds at the monomer-monomer interfaces, decreasing in this way the stability of the TTR tetramer.

molecular biology↗

Modulating Transthyretin Fibril Stability with D-Retro-Inverso Peptides

A major cause of heart failure in elderly patients are deposits of Transthyretin (TTR) fibrils. Using molecular dynamic simulations, we explore how the stability of TTR fibrils can be modulated by D-Retro-Inverso (DRI) Peptides, built from D-amino acids with the sequence of the parent peptide switched, and describe a mechanism by which one of these peptides, DRI-K6V, disrupts TTR fibrils. Our results may open the way to design of peptide drugs targeting established TTR amyloidosis.

biophysics↗

D-Retro-Inverso Peptide Candidates for Inhibiting SAA Cardiac Amyloidosis

In a recent study of a mice model it was suggested that after myocardial infarction Serum Amyloid A (SAA) aggregates are formed that contribute to the long-term complications of the infarct, and that a similar mechanism may exist for humans. Motivated by this hypothesis we have designed four peptide candidates that may interfere with formation of SAA3 fibrils, and using all-atom molecular dynamics have evaluated their ability to destabilize SAA fibrils. As the lifetime of peptide drugs can be increased by replacing L-amino acids with their mirror D-amino acids, we have built the peptides from D-amino acids. We identify two of these peptides, DRI-R5S and DRI-H6A, as promising drug candidates.

biochemistry↗

The Effect of SARS-COV-2 Protein Fragments onthe Dimerization of α-Synuclein

There is evidence that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of -synuclein (S), the main component of brain-located amyloids whose presence is connected with Parkinsons Disease (PD). Using molecular dynamic simulations, we could show in earlier work that SARS-COV-2 protein fragments shift the ensemble of S chains toward more aggregation-prone conformations. However, the mechanism by which these chains assemble into fibrils, the presumed neurotoxic agent in PD, is not clear. The first step on that route are dimers. For this reason, we have now, using again molecular dynamics simulations, studied how the fragment 194FKNIDGYFKI203 (FI10) of the SARS-COV-2 spike protein, and the fragment 54SFYVYSRVK62 (SK9) of the envelope protein, alter the ensemble of -synuclein dimers. Our simulations suggest a differential stabilization of such dimers that would preferentially seed rod-like fibrils over the competing twister-like structures.

molecular biology↗

Modulation of Aβ1-42 Aggregation by a SARS-COV-2 Protein Fragment

A number of studies have pointed out to the possibility that SARS-COV-2 infections could trigger amyloid diseases such as Parkinsons disease or type-II diabetes. In the present study we probe this question for Alzheimers disease which is connected with presence of amyloids rich in A{beta}-peptides. For this purpose, we study by way of molecular dynamics simulations the interaction between the fragment FKNIDGYFKI of the Spike protein with A{beta}1-42 monomer and two fibril models, one patient-derived and one synthetic. Our results are compared with previous studies of other amyloid-forming proteins to identify commonalities and differences in the modulation of amyloid-formation by the viral protein fragment. Table of Contents Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/669385v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@e9d5e7org.highwire.dtl.DTLVardef@1da47baorg.highwire.dtl.DTLVardef@19b1ad4org.highwire.dtl.DTLVardef@1fe5832_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Podoplanin Positive Cell-derived Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction

BackgroundAmyloidosis is a major long-term complication of chronic disease; however, whether it represents one of the complications of post-myocardial infarction (MI) is yet to be fully understood. MethodsUsing wild-type and knocked-out MI mouse models and characterizing in vitro the exosomal communication between bone marrow-derived macrophages and activated mesenchymal stromal cells (MSC) isolated after MI, we investigated the mechanism behind Serum Amyloid A 3 (SAA3) protein overproduction in injured hearts. ResultsHere, we show that amyloidosis occurs after MI and that amyloid fibers are composed of macrophage-derived SAA3 monomers. SAA3 overproduction in macrophages is triggered by exosomal communication from a subset of activated MSC, which, in response to MI, acquire the expression of a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin (PDPN). Cardiac MSCPDPN+ communicate with and activate macrophages through their extracellular vesicles or exosomes. Specifically, MSCPDPN+ derived exosomes (MSCPDPN+ Exosomes) are enriched in SAA3 and exosomal SAA3 protein engages with Toll-like receptor 2 (TRL2) on macrophages, triggering an overproduction and impaired clearance of SAA3 proteins, resulting in aggregation of SAA3 monomers as rigid amyloid deposits in the extracellular space. The onset of amyloid fibers deposition alongside extra-cellular-matrix (ECM) proteins in the ischemic heart exacerbates the rigidity and stiffness of the scar, hindering the contractility of viable myocardium and overall impairing organ function. Using SAA3 and TLR2 deficient mouse models, we show that SAA3 delivered by MSCPDPN+ exosomes promotes post-MI amyloidosis. Inhibition of SAA3 aggregation via administration of a retro-inverso D-peptide, specifically designed to bind SAA3 monomers, prevents the deposition of SAA3 amyloid fibrils, positively modulates the scar formation, and improves heart function post-MI. ConclusionOverall, our findings provide mechanistic insights into post-MI amyloidosis and suggest that SAA3 may be an attractive target for effective scar reversal after ischemic injury and a potential target in multiple diseases characterized by a similar pattern of inflammation and amyloid deposition. NOVELTY AND SIGNIFICANCEWhat is known? O_LIAccumulation of rigid amyloid structures in the left ventricular wall impairs ventricle contractility. C_LIO_LIAfter myocardial infarction cardiac Mesenchymal Stromal Cells (MSC) acquire Podoplanin (PDPN) to better interact with immune cells. C_LIO_LIAmyloid structures can accumulate in the heart after chronic inflammatory conditions. C_LI What information does this article contribute? O_LIWhether accumulation of cumbersome amyloid structures in the ischemic scar impairs left ventricle contractility, and scar reversal after myocardial infarction (MI) has never been investigated. C_LIO_LIThe pathophysiological relevance of PDPN acquirement by MSC and the functional role of their secreted exosomes in the context of post-MI cardiac remodeling has not been investigated. C_LIO_LIAmyloid structures are present in the scar after ischemia and are composed of macrophage-derived Serum Amyloid A (SAA) 3 monomers, although mechanisms of SAA3 overproduction is not established. C_LI SUMMARY OF NOVELTY AND SIGNIFICANCEHere, we report that amyloidosis, a secondary phenomenon of an already preexisting and prolonged chronic inflammatory condition, occurs after MI and that amyloid structures are composed of macrophage-derived SAA3 monomers. Frequently studied cardiac amyloidosis are caused by aggregation of immunoglobulin light chains, transthyretin, fibrinogen, and apolipoprotein in a healthy heart as a consequence of systemic chronic inflammation leading to congestive heart failure with various types of arrhythmias and tissue stiffness. Although chronic MI is considered a systemic inflammatory condition, studies regarding the possible accumulation of amyloidogenic proteins after MI and the mechanisms involved in that process are yet to be reported. Here, we show that SAA3 overproduction in macrophages is triggered in a Toll-like Receptor 2 (TLR2)-p38MAP Kinase-dependent manner by exosomal communication from a subset of activated MSC, which, in response to MI, express a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin. We provide the full mechanism of this phenomenon in murine models and confirm SAA3 amyloidosis in failing human heart samples. Moreover, we developed a retro-inverso D-peptide therapeutic approach, "DRI-R5S," specifically designed to bind SAA3 monomers and prevent post-MI aggregation and deposition of SAA3 amyloid fibrils without interfering with the innate immune response.

immunology↗

In bacterial membranes lipid II changes the stability of pores formed by the antimicrobial peptide nisin

Resistance to available antibiotics poses a growing challenge to modern medicine as this often disallows infections to be controlled. This problem can only be alleviated by developing new drugs. Nisin, a natural lantibiotic with broad antimicrobial activity, has shown promise as a potential candidate for combating antibiotic-resistant bacteria. However, nisin is poorly soluble and barely stable at physiological pH, which, despite attempts to address these issues through mutant design, has restricted its use as a antibacterial drug. Therefore, gaining a deeper understanding of the antimicrobial effectiveness, which relies in part on its ability to form pores, is crucial for finding innovative ways to manage infections caused by resistant bacteria. Using large-scale molecular dynamics simulations we find that the bacterial membrane specific lipid II increases the stability of pores formed by nisin, and that the interplay of nisin and lipid II reduces the overall integrity of bacterial membranes by changing local thickness and viscosity.

biophysics↗

SARS-COV-2 Spike Protein Fragment eases Amyloidogenesis of α-Synuclein

Parkinsons Disease is accompanied by presence of amyloids in the brain formed of -synuclein chains. Correlation between COVID-19 and the onset of Parkinsons disease let to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of -synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, shifts preferentially the ensemble of -synuclein monomer towards rod-like fibril seeding conformations, and at the same time stabilizes differentially this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2.

biochemistry↗

Human Amylin in the Presence of SARS-COV-2 Protein Fragments

Covid-19 can lead to the onset of type-II diabetes which is associated with aggregation of islet amyloid polypeptides, also called amylin. Using molecular dynamics simulations, we investigate how the equilibrium, between amylin monomers in its functional form and fibrils associated with diabetes, is altered in presence of SARS-COV-2 protein fragments. For this purpose, we study the interaction between the fragment SFYVYSRVK of the Envelope protein or the fragment FKNIDGYFKI of the Spike protein with the monomer and two amylin fibril models. Our results are compared with earlier work studying such interactions for two different proteins.

biophysics↗

Effect of an amyloidogenic SARS-COV-2 protein fragment on α-synuclein monomers and fibrils

Using molecular dynamic simulations we study whether amyloidogenic regions in viral proteins can initiate and modulate formation of -synuclein aggregates, thought to be the disease-causing agent in Parkinsons Disease. As an example we choose the nine-residue fragment SFYVYSRVK (SK9), located on the C-terminal of the Envelope protein of SARS-COV-2. We probe how the presence of SK9 affects the conformational ensemble of -synuclein monomers and the stability of two resolved fibril polymorphs. We find that the viral protein fragment SK9 may alter -synuclein amyloid formation by shifting the ensemble toward aggregation-prone and preferentially rod-like fibril seeding conformations. However, SK9 has only little effect of the stability of pre-existing or newly-formed fibrils.

biophysics↗

Interconversion between Serum Amyloid A native and fibril conformations

Overexpression of Serum Amyloid A (SAA) can lead to a form of amyloidosis where the fibrils are made of SAA fragments, most often SAA1-76. Using Replica-Exchange-with-Tunneling, we study the conversion of a SAA1-76 chain between a the folded conformation and a fibril conformation. We find that the basins in the free energy landscape corresponding to the two motifs are separated by barriers of only about 2-3 kBT. Crucial for the assembly into the fibril structure is the salt bridge 26E-34K that provides a scaffold for forming the fibril conformation.

molecular biology↗

The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A

A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. In order to understand whether SAA amyloidosis could also be a long-term risk of SARS-COV-2 infections we have used long all-atom molecular dynamic simulations to study the effect of a SARS-COV-2 protein segment on SAA amyloid formation. Sampling over 40 {micro}s we find that presence of the nine-residue segment SK9, located at the C-terminus of the Envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. Our results therefore suggest that SAA amyloidosis and related pathologies may be a long-term risk of SARS-COV-2 infections.

biophysics↗

Effect of Lauric Acid on the Stability of Abeta-Oligomers

While Alzheimers disease is correlated with the presence of A{beta} fibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation we study how presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded A{beta}42 chains. Such a change would alter the distribution of amyloids in the fatty-acid rich brain environment, and therefore could explain the lower polymorphism observed in A{beta}-fibrils derived from brains of patients with Alzheimers disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.

biophysics↗

Stability of Human Serum Amyloid A Fibrils

In systemic amyloidosis, Serum amyloid A (SAA) fibril deposits cause widespread damages to tissues and organs that eventually may lead to death. A therapeutically intervention therefore has either to dissolve these fibrils or inhibit their formation. However, only recently has the human SAA fibril structure be resolved at a resolution that is sufficient for development of drug candidates. Here, we use molecular dynamic simulations to probe the factors that modulate the stability of this fibril model. Our simulations suggest that fibril formation starts with the stacking of two misfolded monomers into metastable dimers, with the stacking depending on the N-terminal amyloidogenic regions of different chains forming anchors. The resulting dimers pack in a second step into a two-fold two-layer tetramer that is stable enough to nucleate fibril formation. The stability of the initial dimers is enhanced under acidic conditions by a strong salt bridge and side-chain hydrogen bond network in the C-terminal cavity (residues 23 - 51) but not affected by the presence of the disordered C-terminal tail. Table of Content Graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/291948v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@63cb3borg.highwire.dtl.DTLVardef@1b3cd43org.highwire.dtl.DTLVardef@1690125org.highwire.dtl.DTLVardef@ca6162_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Altering the solubility of the antibiotic candidate Nisin - a computational study

The growing bacterial resistance to available antibiotics makes it necessary to look for new drug candidates. An example is a lanthionine-containing nisin, which has a broad spectrum of antimicrobial activity. While nisin is widely utilized as a food preservative, its poor solubility and low stability at physiological pH hinder its use as an antibiotic. As the solubility of nisin is controlled by the residues of the hinge region, we have performed molecular dynamics simulations of various mutants and studied their effects on nisins solubility. These simulations are complicated by the presence of two uncommon residues (dehydroalanine and dehydrobutyrine) in the peptide. The primary goal of the present study is to derive rules for designing new mutants that will be more soluble at physiological pH and, therefore, may serve as a basis for the future antibiotic design. Another aim of our study is to evaluate whether existing force fields can model the solubility of these amino acids accurately, in order to motivate further developments of force fields to account for solubility information.

biophysics↗

Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin

Lymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using Replica-Exchange-with-Tunneling we study the conversion between the two folds. Unlike previously proposed, we find that the fold switching does not require unfolding of Lymphotactin, but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect the {beta}2 and {beta}3 strands and eases the transition between the hydrogen bond pattern by which the central three-stranded {beta}-sheet in the two forms differ.

biophysics↗

D-Retro Inverso (DRI) Amylin and the Stability of Amylin Fibrils

Motivated by the role that amylin aggregates pay in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where L-amino acid chains are replaced by D-Retro Inverso (DRI) amylin, i.e., peptides where the sequence of amino acids is reversed, and at the same time the L-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only marginal difference in fibril structure and stability, aggregating DRI-amylin peptides have different pattern of contacts and hydrogen bonding. Because of these differences does DRI-amylin, when interacting with regular (L) amylin, alter the elongation process and lowers the stability of hybrid amylin fibrils. Our results suggest not only a potential use of DRI-amylin as inhibitor of amylin fibril-formation, but points also to the possibility of using insertion of DRI-proteins in L-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supra-molecular assemblies or aggregates.

molecular biology↗

Cleavage, down-regulation and aggregation of serum amyloid A

Various diseases cause over-expression of the serum amyloid A protein (SAA), which leads in some, but not all, cases to amyloidosis as a secondary disease. The response to the over-expression involves dissociation of SAA hexamer and subsequent cleavage of the released monomers, most commonly yielding fragments SAA1-76 of the full-sized SAA1-104. We report results from molecular dynamic simulations that probe the role of this cleavage for down-regulating activity and the concentration of SAA. We propose a mechanism that relies on two elements. First, the probability to assemble into hexamers is lower for the fragments than it is for the full-sized protein. Second, unlike other fragments SAA1-76 can switch between two distinct configurations. The first kind is easy to proteolyze (allowing a fast reduction of SAA concentration) but prone to aggregation, while the situation is opposite for the second kind. If the time scale for amyloid formation is longer than the one for proteolysis, the aggregation-prone species dominates. However, if environmental conditions such as low pH increase the risk of amyloid formation, the ensemble shifts toward the more protected form. We speculate that SAA amyloidosis is a failure of the switching mechanism leading to accumulation of the aggregation-prone species and subsequent amyloid formation.

biophysics↗