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Papers by Anthony Braun

The treatment is similar to that of simple fluids (1). In the bilayer, com-plications rise due to... more The treatment is similar to that of simple fluids (1). In the bilayer, com-plications rise due to the coupling of the two monolayers and fluctuations of the lipid/water interface. For each monolayer surface, we define the local height and local number density z(r) = a N∑ l=1 z(rl) δ(r − rl) (S1.1) ρ(r) = N∑ l=1 δ(r − rl) , (S1.2) from the positions rl = (xl, yl) of the N constituent lipid molecules. The Fourier transforms are z(q) = 1 N N∑ l=1 z(rl) e −iq·rl (S1.3) ρ(q) =

ACS chemical neuroscience, Sep 10, 2017

The first structures of α-synuclein (αSyn) fibrils have recently been solved. Here, we use a uniq... more The first structures of α-synuclein (αSyn) fibrils have recently been solved. Here, we use a unique combination of molecular dynamics simulation strategies to address the minimal nucleation size of the 11-amino acid NAC protofibril solved by X-ray and to interrogate the dynamic behavior of unexpected crystal waters in the steric zipper. We found that protofibrils of >8 chains are thermodynamically stabilized due to protection of the fibril core from solvent influx and ordering of the end strands by the fibril core. In these stable oligomers, water molecules resolved in the crystal structure freely exchange with bulk solvent but are, on average, stably coordinated along the β-sheet by inward-facing Thr72 and Thr75. We confirm the persistence of this water coordination via simulations of the full-length Greek-key structure solved by NMR and speculate that these Thr-water networks are important in the context of enhanced fibril nucleation in the familial A53T mutation.

Determination of electron density pro les and area-per-lipid from molecular dynamics simulations ... more Determination of electron density pro les and area-per-lipid from molecular dynamics simulations of large undulating lipid bilayers

Biophysical Journal, 2018

Aggregation of endogenous a-synuclein is the hallmark of Parkinson's disease pathology. Under nor... more Aggregation of endogenous a-synuclein is the hallmark of Parkinson's disease pathology. Under normal conditions, a-synuclein plays an important role in neurological function. Under pathologic conditions, misfolded a-synuclein forms cytotoxic oligomers and fibrils. There has been significant effort to identify small molecule inhibitors of a-synuclein fibrillization. However, recent evidence suggests the kinetically unstable oligomeric species, and not fibrils, are the source of a-synuclein cytotoxicity. We interrogated the selfassociation of the oligomeric species under aggregation prone conditions using FRET. To achieve this, we developed a set of cell-free FRET based biosensors that monitor oligomer-oligomer interactions and fibril formation through fluorescence lifetime. Using fluorescence lifetime provides a 30-fold increase in sensitivity over more traditional FRET measurements. We have achieved an optimal FRET of 14.99% for oligomeric interactions and a seeded induced change in FRET of 15.34%. We are currently optimizing these biosensors for scale up to facilitate high throughput screening. Hits will be validated for FRET dose response and biophysical changes in aggregation kinetics via thioflavin T assays and AFM characterization.

Alzheimer's & Dementia, 2019

Objective-Understanding the heterogeneous pathology in Alzheimer's disease (AD) and related tauop... more Objective-Understanding the heterogeneous pathology in Alzheimer's disease (AD) and related tauopathies is one of the most urgent and fundamental challenges facing the discovery of novel disease modifying therapies. Through monitoring ensembles of toxic and non-toxic tau oligomers spontaneously formed in cells, our biosensor technology can identify tool compounds that

The Journal of membrane biology, Jan 27, 2018

The original version of the article unfortunately contained error in author group; two authors we... more The original version of the article unfortunately contained error in author group; two authors were not submitted and published in the original version. Also the funding information is erroneously omitted.

Journal of chemical theory and computation, Jan 9, 2014

We have developed an algorithm to determine membrane structure, area per lipid, and bending rigid... more We have developed an algorithm to determine membrane structure, area per lipid, and bending rigidity from molecular dynamics simulations of lipid vesicles. Current methods to extract structure from vesicle simulations define densities relative to the global center of mass of the vesicle. This approach ignores the long-wavelength fluctuations (undulations) that develop across the sphere and broaden the underlying structure. Our method establishes a local reference frame by defining a radially undulating reference surface (URS) and thereby removes the broadening effect of the undulations. Using an arc-length low-pass filter, we render the URS by defining the bilayer midplane on an equi-angular θ, ϕ-grid (colatitude, longitude). This surface is then expanded onto a truncated series of spherical harmonics. The spherical harmonic coefficients characterize the long-wavelength fluctuations that define both the local reference frame-used to determine the bilayer's structure-and the area...

The Journal of Membrane Biology, 2011

It is generally accepted that ions interact directly with lipids in biological membranes. Decades... more It is generally accepted that ions interact directly with lipids in biological membranes. Decades of biophysical studies on pure lipid bilayer systems have shown that only certain types of ions, most significantly large anions and multivalent cations, can fundamentally alter the structure and dynamics of lipid bilayers. It has long been accepted that at physiological concentrations NaCl ions do not alter the physical behavior or structure of bilayers composed solely of zwitterionic phosphatidylcholine (PC) lipids. Recent X-ray scattering experiments have reaffirmed this dogma, showing that below 1 M concentration, NaCl does not significantly alter bilayer structure. However, despite this history, there is an ongoing controversy within the molecular dynamics (MD) simulation community regarding NaCl/PC interactions. In particular, the CHARMM and GROMOS force fields show dramatically different behavior, including the effect on bilayer structure, surface potential, and the ability to form stable, coordinated ion-lipid complexes. Here, using longtimescale, constant-pressure simulations under the newest version of the CHARMM force field, we find that Na ? and Classociate with PC head groups in a POPC bilayer with approximately equal, though weak, affinity, and that the salt has a negligible effect on bilayer structure, consistent with earlier CHARMM results and more recent X-ray data. The results suggest that interpretation of simulations where lipids interact with charged groups of any sort, including charged proteins, must be carefully scrutinized.

Biophysical Journal, 2010

Annual Reports in Computational Chemistry, 2011

Atomistic molecular dynamics (MD) simulations are a powerful computational tool for probing the a... more Atomistic molecular dynamics (MD) simulations are a powerful computational tool for probing the atomic-scale details of phospholipid bilayer structure and dynamics. Careful validation of the simulations is a critical step if the simulator is to establish productive contact with the experimentalist. The most fruitful approach is to directly compare simulated properties that correspond to primary experimental data, rather than to

University of Minnesota Ph.D. dissertation. July 2014. Major: Biomedical Engineering. Advisor: Jo... more University of Minnesota Ph.D. dissertation. July 2014. Major: Biomedical Engineering. Advisor: Johnathan N. Sachs. 1 computer file (PDF); xviii, 253 pages.

npj Parkinson's Disease

We have developed a high-throughput drug discovery platform, measuring fluorescence resonance ene... more We have developed a high-throughput drug discovery platform, measuring fluorescence resonance energy transfer (FRET) with fluorescent alpha-synuclein (αSN) biosensors, to detect spontaneous pre-fibrillar oligomers in living cells. Our two αSN FRET biosensors provide complementary insight into αSN oligomerization and conformation in order to improve the success of drug discovery campaigns for the treatment of Parkinson’s disease. We measure FRET by fluorescence lifetime, rather than traditional fluorescence intensity, providing a structural readout with greater resolution and precision. This facilitates identification of compounds that cause subtle but significant conformational changes in the ensemble of oligomeric states that are easily missed using intensity-based FRET. We screened a 1280-compound small-molecule library and identified 21 compounds that changed the lifetime by >5 SD. Two of these compounds have nanomolar potency in protecting SH-SY5Y cells from αSN-induced death...

ABSTRACTPreventing or reversing the pathological misfolding and self-association of alpha-synucle... more ABSTRACTPreventing or reversing the pathological misfolding and self-association of alpha-synuclein (aSyn) can rescue a broad spectrum of pathological cellular insults that manifest in Parkinson’s Disease (PD), Dementia with Lewy bodies (DLB), and other alpha-synucleinopathies. We have developed a high-throughput, FRET-based drug discovery platform that combines high-resolution protein structural detection in living cells with an array of functional and biophysical assays to identify novel lead compounds that protect SH-SY5Y cells from aSyn induced cytotoxicity as well as inhibiting seeded aSyn aggregation, even at nanomolar concentrations.Our combination of cellular and cell-free assays allow us to distinguish between direct aSyn binding or indirect mechanisms of action (MOA). We focus on targeting oligomers with the requisite sensitivity to detect subtle protein structural changes that may lead to effective therapeutic discoveries for PD, DLB, and other alpha-synucleinopathies. Pi...

Biophysical Journal

covalently modifying the His residues of Ab proteins. The acceleration is likely due to an increa... more covalently modifying the His residues of Ab proteins. The acceleration is likely due to an increased affinity of the Ab protein for the membrane surface where fibril formation is effectively nucleated. HHE, in contrast, has no such effect, most likely because the shorter hydrophobic chains of HHE are not effective at anchoring the protein to the membrane. We recently demonstrated that oxidative ARA degradation, and hence HNE production, was actively occurring only in regions of the human Alzheimer's disease (AD) brain where amyloid plaques were present.

Tauopathies, including Alzheimer’s disease, are a group of neurodegenerative disorders characteri... more Tauopathies, including Alzheimer’s disease, are a group of neurodegenerative disorders characterized by pathological aggregation of the microtubule binding protein tau. Recent studies suggest that toxic tau oligomers, which are soluble and distinct from insoluble beta-sheet fibrils, are central players in neuronal cell death. To exploit this new therapeutic window, we engineered two first-in-class FRET based biosensors that monitor tau conformations in cells. Because this new technology platform operates in cells, it enables high-throughput screening of small molecules that target tau oligomers while avoiding the uncertainties of idiosyncratic in vitro preparations of tau assemblies from purified protein. We found a small molecule, MK-886, that disrupts tau oligomers and reduces tau-induced cell cytotoxicity with nanomolar potency. Using SPR and an advanced single-molecule FRET technique, we show that MK-886 directly binds to tau and specifically perturbs the folding of tau monomer ...

Biochimica et Biophysica Acta (BBA) - Biomembranes

Using molecular dynamics simulations, we have explored the effect of asymmetric lipidsspecificall... more Using molecular dynamics simulations, we have explored the effect of asymmetric lipidsspecifically those that contain one polyunsaturated (PUFA) and one saturated fatty acid chain-on phase separation in heterogeneous membranes. These lipids are prevalent in neuronal membranes, particularly in synaptic membranes, where the Parkinson's Disease protein α-Synuclein (αS) is found. We have therefore explored the relationship between asymmetric, PUFA-containing lipids, and αS. The simulations show that asymmetric lipids partition to the liquid disordered (Ld) phase of canonical raft mixtures because of the highly disordered PUFA chain. In the case of a membrane built to mimic the lipid composition of a synaptic vesicle, the PUFA-containing asymmetric lipids completely disrupt phase separation. Because αS is positively charged, we show that it partitions with negatively charged lipids, regardless of the saturation state of the chains. Additionally, αS preferentially associates with the polyunsaturated fatty acid tails of both charged and neutral lipids. This is a consequence of those chains' ability to accommodate the void beneath the amphipathic helix. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.

Journal of molecular biology, Dec 6, 2016

Death receptor 5 (DR5) is an apoptosis-inducing member of the tumor necrosis factor superfamily, ... more Death receptor 5 (DR5) is an apoptosis-inducing member of the tumor necrosis factor superfamily, whose activity has been linked to membrane cholesterol content. Upon ligand binding, DR5 forms large clusters within the plasma membrane that have often been assumed to be manifestations of receptor co-localization in cholesterol-rich membrane domains. However, we have recently shown that DR5 clusters are more than just randomly aggregated receptors. Instead, these are highly structured networks held together by receptor dimers. These dimers are stabilized by specific transmembrane helix-helix interactions, including a disulfide bond in the long isoform of the receptor. The complex relationship among DR5 network formation, transmembrane helix dimerization, membrane cholesterol, and receptor activity has not been established. It is unknown whether the membrane itself plays an active role in driving DR5 transmembrane helix interactions or in the formation of the networks. We show that chol...

The Journal of Biological Chemistry, Apr 10, 2012

Background: Whether ligand-induced clusters of DR5 have a specific structural organization is unk... more Background: Whether ligand-induced clusters of DR5 have a specific structural organization is unknown. Results: Ligand binding results in the formation of death receptor dimers that exist within high molecular weight networks. Conclusion: Ligand-induced DR5 clusters are highly organized networks formed through dimerization of receptor trimers. Significance: The biophysical character of DR5 networks may have implications for future rational design of DR5-targeted therapeutics. Recent evidence suggests that TNF-related apoptosis-inducing ligand (TRAIL), a death-inducing cytokine with anti-tumor potential, initiates apoptosis by reorganizing TRAIL receptors into large clusters, although the structure of these clusters and the mechanism by which they assemble are unknown. Here, we demonstrate that TRAIL receptor 2 (DR5) forms receptor dimers in a ligand-dependent manner at endogenous receptor levels, and these receptor dimers exist within high molecular weight networks. Using mutational analysis, FRET, fluorescence microscopy, synthetic biochemistry, and molecular modeling, we find that receptor dimerization relies upon covalent and noncovalent interactions between membrane-proximal residues. Additionally, by using FRET, we show that the oligomeric structure of two functional isoforms of DR5 is indistinguishable. The resulting model of DR5 activation should revise the accepted architecture of the functioning units of DR5 and the structurally homologous TNF receptor superfamily members.

Biochimica et biophysica acta, Jan 10, 2016

We review experimental and simulation approaches that have been used to determine curvature gener... more We review experimental and simulation approaches that have been used to determine curvature generation and remodeling of lipid bilayers by membrane-bending proteins. Particular emphasis is placed on the complementary approaches used to study α-Synuclein (αSyn), a major protein involved in Parkinson's disease (PD). Recent cellular and biophysical experiments have shown that the protein 1) deforms the native structure of mitochondrial and model membranes; and 2) inhibits vesicular fusion. Today's advanced experimental and computational technology has made it possible to quantify these protein-induced changes in membrane shape and material properties. Collectively, experiments, theory and multi-scale simulation techniques have established the key physical determinants of membrane remodeling and rigidity: protein binding energy, protein partition depth, protein density, and membrane tension. Despite the exciting and significant progress made in recent years in these areas, chall...

Biophys J, 2009

Alpha-synuclein remains a protein of interest due to its propensity to form fibrillar aggregates ... more Alpha-synuclein remains a protein of interest due to its propensity to form fibrillar aggregates in neurodegenerative disease and its putative function in synaptic vesicle regulation. Herein, we present a series of atomistic molecular dynamics simulations of wild-type alpha-synuclein and three Parkinson disease familial mutants (A30P, A53T, and E46K) in two distinct environments. First, in order to match recent NMR experiments, we have simulated each protein bound to an SDS detergent micelle. Second, in order to connect more closely to the true biological environment, we have simulated the proteins bound to a 1,2-dioleoyl-sn-glycero-3-phosphoserine lipid bilayer. In the micelle-bound case, we find that the wild type and all of the variants of alpha-synuclein flatten the underlying micelle, decreasing its surface area. A30P is known to lessen alpha-synuclein/membrane affinity and, consistent with experiment, destabilizes the simulated secondary structure. In the case of A53T, our simulations reveal a range of stabilizing hydrogen bonds that form with the threonine. In both environments, the E46K mutation, which is known to increase bilayer affinity, leads to an additional hydrogen bond between the protein and either the detergent or lipid. Simulations indicate that alphaS and its variants are less dynamic in the bilayer than in the micelle. Furthermore, the simulations of the mutants suggest how changes in the structure and dynamics of alpha-synuclein may affect its biological role.