Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein

The evolution of the Amber additive protein force field: History, current status, and future

Molecular dynamics simulations are pivotal in elucidating the intricate properties of biological molecules. Nonetheless, the reliability of their outcomes hinges on the precision of the molecular force field utilized. In this perspective, we present a comprehensive review of the developmental trajectory of the Amber additive protein force field, delving into researchers' persistent quest for higher precision force fields and the prevailing challenges. We detail the parameterization process of the Amber protein force fields, emphasizing the specific improvements and retained features in each version compared to their predecessors. Furthermore, we discuss the challenges that current force fields encounter in balancing the interactions of protein-protein, protein-water, and water-water in molecular dynamics simulations, as well as potential solutions to overcome these issues.

Molecular dynamics simulation of wild and mutant proteasome subunit beta type 8 (PSMB8) protein: Implications for restoration of inflammation in experimental autoimmune encephalomyelitis pathogenesis

Multiple Sclerosis (MS) is an autoimmune and chronic disease in the brain and spinal cord. MS has inflammatory progression characterized by its hallmark inflammatory plaques. The histological and clinical characteristics of MS are shared by Experimental Autoimmune Encephalomyelitis (EAE). Genetic and environmental factors contribute to the development of MS. In EAE-MS disease, the level of proteasome subunit beta type-8 (PSMB8), encoded by the PSMB8 gene, is increased and regulates the inflammatory response in this disease. In humans, the Nakajo-Nishimura Syndrome is caused by a mutation in the gene PSMB8, a part of the immunoproteasome subunit. Therefore, special attention to wild and mutant (G210V) PSMB8 protein is imperative. In this study, we performed a 100 ns molecular dynamics (MD) simulation for wild-type PSMB8 and the mutant G210V. Then, we analyzed the fundamental and essential simulation results using another Google Colab system. The energy analysis ensures the structural deviation due to point mutation. The trajectory of the fundamental simulation (RMSD, RMSF, and Rg) describes that the G210V mutated protein is more flexible and less stable than the wild type. We observed the conformational changes due to mutation by analyzing the RMSD average linkage hierarchical clustering, total SASA, and SASA autocorrelation. The differences in the protein's overall motion and the atoms' precise location are identified by the principal component analysis, showing that the overall motion and location of the atoms are different. Our study provides valuable insights into the dynamics and structure of this protein, which can aid in further understanding its biological functions and potential implications for disease.

Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer

To propose new mechanism-based therapeutics for Alzheimer's disease (AD), it is crucial to study the kinetics and oligomerization/aggregation mechanisms of the hallmark tau proteins, which have various isoforms and are intrinsically disordered. In this study, multiple all-atom (AA) and coarse-grained (CG) force fields (FFs) have been benchmarked on molecular dynamics (MD) simulations of K18 tau (M243-E372), which is a truncated form (130 residues) of full-length tau (441 residues). FF19SB is first excluded because the dynamics are too slow, and the conformations are too stable. All other benchmarked AAFFs (Charmm36m, FF14SB, Gromos54A7, and OPLS-AA) and CGFFs (Martini3 and Sirah2.0) exhibit a trend of shrinking K18 tau into compact structures with the radius of gyration (ROG) around 2.0 nm, which is much smaller than the experimental value of 3.8 nm, within 200 ns of AA-MD or 2000 ns of CG-MD. Gromos54A7, OPLS-AA, and Martini3 shrink much faster than the other FFs. To perform meaningful postanalysis of various properties, we propose a strategy of selecting snapshots with 2.5 < ROG < 4.5 nm, instead of using all sampled snapshots. The calculated chemical shifts of all C, CA, and CB atoms have very good and close root-mean-square error (RMSE) values, while Charmm36m and Sirah2.0 exhibit better chemical shifts of N than other FFs. Comparing the calculated distributions of the distance between the CA atoms of CYS291 and CYS322 with the results of the FRET experiment demonstrates that Charmm36m is a perfect match with the experiment while other FFs exhibit limitations. In summary, Charmm36m is recommended as the best AAFF, and Sirah2.0 is recommended as an excellent CGFF for simulating tau K18.

Comprehending the Efficacy of Whitlock's Caffeine-Pincered Molecular Tweezer on β-Amyloid Aggregation

Alzheimer's disease (AD) stands as one of the most prevalent neurodegenerative conditions, leading to cognitive impairment, with no cure and preventive measures. Misfolding and aberrant aggregation of amyloid-β (Aβ) peptides are believed to be the underlying cause of AD. These amyloid aggregates culminate in the development of toxic Aβ oligomers and subsequent accumulation of β-amyloid plaques amidst neuronal cells in the brain, marking the hallmarks of AD. Drug development for the potentially curative treatment of Alzheimer's is, therefore, a tremendous challenge for the scientific community. In this study, we investigate the potency of Whitlock's caffeine-armed molecular tweezer in combating the deleterious effects of Aβ aggregation, with special emphasis on the seven residue Aβ16-22 fragment. Extensive all-atom molecular dynamics simulations are conducted to probe the various structural and conformational transitions of the peptides in an aqueous medium in both the presence and absence of tweezers. To explore the specifics of peptide-tweezer interactions, radial distribution functions, contact number calculations, binding free energies, and 2-D kernel density plots depicting the variation of distance-angle between the aromatic planes of the peptide-tweezer pair are computed. The central hydrophobic core, particularly the aromatic Phe residues, is crucial in the development of harmful amyloid oligomers. Notably, all analyses indicate reduced interpeptide interactions in the presence of the tweezer, which is attributed to the tweezer-Phe aromatic interaction. Upon increasing the tweezer concentration, the residues of the peptide are further encased in a hydrophobic environment created by the self-aggregating tweezer cluster, leading to the segregation of the peptide residues. This is further aided by the weakening of interstrand hydrogen bonding between the peptides, thereby impeding their self-aggregation and preventing the formation of neurotoxic β-amyloid. Furthermore, the study also highlights the efficacy of the molecular tweezer in destabilizing preformed amyloid fibrils as well as hindering the aggregation of the full-length Aβ1-42 peptide.

Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies

Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations

The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the β-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of β-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding.

Role of G326 in Determining the Aggregation Propensity of R3 Tau Repeat: Insights from Studies on R1R3 Tau Construct

The Microtubule-binding repeat region (MTBR) of Tau has been studied extensively due to its pathological implications in neurodegenerative diseases like Alzheimer's disease. The pathological property of MTBR is mainly due to the R3 repeat's high propensity for self-aggregation, highlighting the critical molecular grammar of the repeat. Utilizing the R1R3 construct (WT) and its G326E mutant (EE), we determine the distinct characteristics of various peptide segments that modulate the aggregation propensity of the R3 repeat using NMR spectroscopy. Through time-dependent experiments, we have identified 317KVTSKCGS324 in R3 repeat as the aggregation initiating motif (AIM) due to its role at the initial stages of aggregation. The G326E mutation induces changes in conformation and dynamics at the AIM, thereby effectively abrogating the aggregation propensity of the R1R3 construct. We further corroborate our findings through MD simulations and propose that AIM is a robust site of interest for tauopathy drug design.

Construction of High Accuracy Machine Learning Interatomic Potential for Surface/Interface of Nanomaterials-A Review

The inherent discontinuity and unique dimensional attributes of nanomaterial surfaces and interfaces bestow them with various exceptional properties. These properties, however, also introduce difficulties for both experimental and computational studies. The advent of machine learning interatomic potential (MLIP) addresses some of the limitations associated with empirical force fields, presenting a valuable avenue for accurate simulations of these surfaces/interfaces of nanomaterials. Central to this approach is the idea of capturing the relationship between system configuration and potential energy, leveraging the proficiency of machine learning (ML) to precisely approximate high-dimensional functions. This review offers an in-depth examination of MLIP principles and their execution and elaborates on their applications in the realm of nanomaterial surface and interface systems. The prevailing challenges faced by this potent methodology are also discussed.

Elucidating the reversible and irreversible self-assembly mechanisms of low-complexity aromatic-rich kinked peptides and steric zipper peptides

Many RNA-binding proteins such as fused-in sarcoma (FUS) can self-assemble into reversible liquid droplets and fibrils through the self-association of their low-complexity (LC) domains. Recent experiments have revealed that SYG-rich segments in the FUS LC domains play critical roles in the reversible self-assembly behaviors of FUS. These FUS LC segments alone can self-assemble into reversible kinked fibrils, which are markedly different from the canonical irreversible steric zipper β-sheet fibrils. However, the molecular determinants underlying the reversible and irreversible self-assembly are poorly understood. Herein we conducted extensive all-atom and coarse-grained molecular dynamics simulations of four representative hexapeptides: two low-complexity aromatic-rich kinked peptides from the amyotrophic lateral sclerosis-related FUS protein, FUS37-42 (SYSGYS) and FUS54-59 (SYSSYG); and two steric zipper peptides from Alzheimer's-associated Aβ and Tau proteins, Aβ16-21 (KLVFFA) and Tau306-311 (VQIVYK). We dissected their reversible and irreversible self-assembly dynamics, predicted their phase separation behaviors, and elucidated the underpinning molecular interactions. Our simulations showed that alternating stickers (Tyr) and spacers (Gly and Ser) in FUS37-42 and FUS54-59 facilitate the formation of highly dynamic coil-rich oligomers and lead to reversible self-assembly, while consecutive hydrophobic residues of LVFF in Aβ16-21 and IVY in Tau306-311 act as hydrophobic patches, favoring the formation of stable β-sheet-rich oligomers and driving the irreversible self-assembly. Intriguingly, we found that FUS37-42 and FUS54-59 peptides, possessing the same amino acid composition and the same number of sticker and spacer residues, display differential self-assembly propensities. This finding suggests that the self-assembly behaviors of FUS peptides are fine-tuned by the site-specific patterning of spacer residues (Ser and Gly). This study provides significant mechanistic insights into reversible and irreversible peptide self-assembly, which would be helpful for understanding the molecular mechanisms underlying the formation of biological liquid condensates and pathological solid amyloid fibrils.

Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6

The PHF6 (Val-Gln-Ile-Val-Tyr-Lys) motif, found in all isoforms of the microtubule-associated protein tau, forms an integral part of ordered cores of amyloid fibrils formed in tauopathies and is thought to play a fundamental role in tau aggregation. Because PHF6 as an isolated hexapeptide assembles into ordered fibrils on its own, it is investigated as a minimal model for insight into the initial stages of aggregation of larger tau fragments. Even for this small peptide, however, the large length and time scales associated with fibrillization pose challenges for simulation studies of its dynamic assembly, equilibrium configurational landscape, and phase behavior. Here, we develop an accurate, bottom-up coarse-grained model of PHF6 for large-scale simulations of its aggregation, which we use to uncover molecular interactions and thermodynamic driving forces governing its assembly. The model, not trained on any explicit information about fibrillar structure, predicts coexistence of formed fibrils with monomers in solution, and we calculate a putative equilibrium phase diagram in concentration-temperature space. We also characterize the configurational and free energetic landscape of PHF6 oligomers. Importantly, we demonstrate with a model of heparin that this widely studied cofactor enhances the aggregation propensity of PHF6 by ordering monomers during nucleation and remaining associated with growing fibrils, consistent with experimentally characterized heparin-tau interactions. Overall, this effort provides detailed molecular insight into PHF6 aggregation thermodynamics and pathways and, furthermore, demonstrates the potential of modern multiscale modeling techniques to produce predictive models of amyloidogenic peptides simultaneously capturing sequence-specific effects and emergent aggregate structures.

Identification of Aggregation Mechanism of Acetylated PHF6* and PHF6 Tau Peptides Based on Molecular Dynamics Simulations and Markov State Modeling

The microtubule-associated protein tau (MAPT) has a critical role in the development and preservation of the nervous system. However, tau's dysfunction and accumulation in the human brain can lead to several neurodegenerative diseases, such as Alzheimer's disease, Down's syndrome, and frontotemporal dementia. The microtubule binding (MTB) domain plays a significant, important role in determining the tau's pathophysiology, as the core of paired helical filaments PHF6* (275VQIINK280) and PHF6 (306VQIVYK311) of R2 and R3 repeat units, respectively, are formed in this region, which promotes tau aggregation. Post-translational modifications, and in particular lysine acetylation at K280 of PHF6* and K311 of PHF6, have been previously established to promote tau misfolding and aggregation. However, the exact aggregation mechanism is not known. In this study, we established an atomic-level nucleation-extension mechanism of the separated aggregation of acetylated PHF6* and PHF6 hexapeptides, respectively, of tau. We show that the acetylation of the lysine residues promotes the formation of β-sheet enriched high-ordered oligomers. The Markov state model analysis of ac-PHF6* and ac-PHF6 aggregation revealed the formation of an antiparallel dimer nucleus which could be extended from both sides in a parallel manner to form mixed-oriented and high-ordered oligomers. Our study describes the detailed mechanism for acetylation-driven tau aggregation, which provides valuable insights into the effect of post-translation modification in altering the pathophysiology of tau hexapeptides.

Interaction of bioactive kaempferol with HMGB1: Investigation by multi-spectroscopic and molecular simulation methods

Chronic and persistent inflammation associated with excessive high mobility group protein 1 (HMGB1) is a risk factor for various diseases. Dietary intake of kaempferol has been proven to be effective in reducing HMGB1 levels and the degree of inflammation, but the structural mechanism remains unclear. In this context, we first investigated the interaction between bioactive kaempferol and HMGB1 using multi-spectroscopic and molecular simulation techniques. The surface plasmon resonance (SPR) data indicated that kaempferol binds directly to HMGB1 with a K_d value of 2.89 × 10^-5 M. Binding of kaempferol with HMGB1 led to the intrinsic fluorescence quenching and modest secondary structure change of HMGB1 supported by fluorescence spectrometry and circular dichroism (CD). Using dynamic light scattering (DLS), it was found that kaempferol induced the aggregation of HMGB1 protein complex to form larger particles. On HMGB1-activated RAW264.7 cells, kaempferol co-incubation exhibited a remarkable inhibitory effect on nitric oxide (NO) release with an IC₅₀ value of 5.02 μM, which was lower than that of quercetin. In silico, kaempferol binds to HMGB1 mainly through hydrogen bonds and hydrophobic forces. Collectively, our study showed kaempferol as a potential HMGB1 inhibitor, mainly acting by direct binding to HMGB1 and inducing its conformational changes, which provides clues for the treatment of chronic inflammation by kaempferol.

Interaction of the tau fibrils with the neuronal membrane

Tau proteins are recently gaining a lot of interest due to their active role in causing a range of tauopathies. Molecular mechanisms underlying the tau interaction with the neuronal membrane are hitherto unknown and difficult to characterize using experimental methods. Using the cryo-EM structure of the tau-fibrils we have used atomistic molecular dynamics simulation to model the tau fibril and neuronal membrane interaction using explicit solvation. The dynamics and structural characteristics of the tau fibril with the neuronal membrane are compared to the tau fibril in the aqueous phase to corroborate the effect of the neuronal membrane in the tau structure. Tau fibrils have been modelled using CHARMM-36m force field and the six component neuronal membrane composition is taken from the earlier simulation results. The timescale conceivable in our molecular dynamics simulations is of the order of microseconds which captures the onset of the interaction of the tau fibrils with the neuronal membrane. This interaction is found to impact the tau pathogenesis that finally causes neuronal toxicity. Our study initiates the understanding of tau conformational ensemble in the presence of neuronal membrane and sheds the light on the significant tau-membrane interactions.

Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers

Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.

Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2

In tauopathies such as Alzheimer's disease (AD), aberrant phosphorylation causes the dissociation of tau proteins from microtubules. The dissociated tau then aggregates into sequent forms from soluble oligomers to paired helical filaments and insoluble neurofibrillary tangles (NFTs). NFTs is a hallmark of AD, while oligomers are found to be the most toxic form of the tau aggregates. Therefore, understanding tau oligomerization with regard to abnormal phosphorylation is important for the therapeutic development of AD. In this study, we investigated the impact of phosphorylated Ser289, one of the 40 aberrant phosphorylation sites of full-length tau proteins, on monomeric and dimeric structures of tau repeat R2 peptides. We carried out intensive replica exchange molecular dynamics simulation with a total simulation time of up to 0.1 ms. Our result showed that the phosphorylation significantly affected the structures of both the monomer and the dimer. For the monomer, the phosphorylation enhanced ordered-disordered structural transition and intramolecular interaction, leading to more compactness of the phosphorylated R2 compared to the wild-type one. As to the dimer, the phosphorylation increased intermolecular interaction and β-sheet formation, which can accelerate the oligomerization of R2 peptides. This result suggests that the phosphorylation at Ser289 is likely to promote tau aggregation. We also observed a phosphorylated Ser289-Na+-phosphorylated Ser289 bridge in the phosphorylated R2 dimer, suggesting an important role of cation ions in tau aggregation. Our findings suggest that phosphorylation at Ser289 should be taken into account in the inhibitor screening of tau oligomerization.

Atomistic Insights into the Inhibitory Mechanism of Tyrosine Phosphorylation against the Aggregation of Human Tau Fragment PHF6

Abnormal aggregation of the microtubule-associated protein tau into intracellular fibrillary inclusions is characterized as the hallmark of tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. The hexapeptide ³⁰⁶VQIVYK³¹¹ (PHF6) of R3 plays an important role in the aggregation of tau. Recent experimental studies reported that phosphorylation of residue tyrosine 310 (Y310) could decrease the propensity of PHF6 to form fibrils and inhibit tau aggregation. However, the underlying inhibitory mechanism is not well understood. In this work, we systematically investigated the influences of phosphorylation on the conformational ensembles and oligomerization dynamics of PHF6 by performing extensive all-atom molecular dynamics (MD) simulations. Our replica exchange MD simulations demonstrate that Y310 phosphorylation could effectively suppress the formation of β-structure and shift PHF6 oligomers toward coil-rich aggregates. The interaction analyses show that hydrogen bonding and hydrophobic interactions among PHF6 peptides, as well as Y310-Y310 π-π stacking and I308-Y310 CH-π interactions, are weakened by phosphorylation. Additional microsecond MD simulations show that Y310 phosphorylation could inhibit the oligomerization of PHF6 by preventing the formation of large β-sheet oligomers and multi-layer β-sheet aggregates. This study provides mechanistic insights into the phosphorylation-inhibited tau aggregation, which may be helpful for the in-depth understanding of the pathogenesis of tauopathies.

Sequence-Dependent Conformational Properties of PGGG Motif in Tau Repeats: Insights from Molecular Dynamics Simulations of Narrow Pick Filament

Tauopathies are a class of neurodegenerative diseases correlated with the presence of pathological Tau fibrils as a diagnostic marker. The microtubule-binding repeat region of Tau protein, which includes R1, R2, R3, and R4 repeats, constitutes the core of these fibrils. Each repeat consists of a semiconserved C-terminal hexapeptide flanked by KxGS and PGGG motifs. Previous studies have shown the influence of these peptides on protein aggregation, yet their repeat-specific properties are less explored. Using molecular dynamics, we probed the sequence-specific influence of the C-terminal hexapeptide (²⁶⁴ENLKHQ²⁶⁹) in determining the compact local conformation of the R1 repeat of the narrow Pick filament (NPF) with a homologous E264G mutation. In addition to that, we also studied the influence of ²⁶²S phosphorylation on this conformation as the phosphorylation is proposed to alleviate the pathogenesis of Pick's disease. Interestingly, we determined that E264G mutation induces a conformational shift of ²⁷⁰PGGG²⁷³ from a turn to a random coil. This conformational dependence is experimentally verified with the R1R3-E264G mutant construct, which displayed accelerated aggregation compared with the R1R3 wild-type construct. A significant delay in aggregation of the R1R3-G326E mutant further demonstrates the importance of ³²⁶G in determining the conformation of the R3 repeat. Thus, we conclude that the conformational properties of the PGGG motif in Tau repeats are strongly dependent on the repeat-specific sequence of the C-terminal hexapeptide.

A Guide to In Silico Drug Design

The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.

Disparate Effect of Hybrid Peptidomimetics Containing Isomers of Aminobenzoic Acid on hIAPP Aggregation

The abnormal misfolding of human islet amyloid polypeptide (hIAPP) in pancreatic β-cells is implicated in the progression of type II diabetes (T2D). With the prevalence of T2D increasing worldwide, preventing the aggregation of hIAPP has been recognized as a promising therapeutic strategy to control this disease. Recently, a class of novel conformationally restricted β-sheet breaker hybrid peptidomimetics (BSBHps) was found to demonstrate efficient inhibitory ability toward amyloid formation of hIAPP. One (Ile26) or more (Gly24 and Ile26) residues in these six-membered peptide sequences, which have been extracted from the amyloidogenic core of hIAPP, N₂₂FGAIL₂₇, are substituted by three different isomers of the conformationally restricted aromatic amino acid, i.e., aminobenzoic acid (β, γ, and δ), to generate these BSBHps. The presence of the nonproteinogenic aminobenzoic acid moiety renders the BSBHps to be more stable toward proteolytic degradation. The different isomeric BSBHps exhibit contrasting influence on the self-assembly of hIAPP. The BSBHps containing β- and γ-aminobenzoic acid can sufficiently prevent hIAPP aggregation, but those with the δ-aminobenzoic group stabilize the β-sheet-rich aggregate of hIAPP. The difference in the angle between the amino and carboxyl groups in the isomers of the aminobenzoic moiety causes the BSBHps to attain discrete conformation and hence leads to variation in their binding preference with hIAPP and ultimately their inhibitory potency. This guides the pathway for the dissimilar effect of BSBHps on peptide aggregation and, therefore, provides insights into the design considerations for novel drugs against T2D.

Atomistic Insights into A315E Mutation-Enhanced Pathogenicity of TDP-43 Core Fibrils

The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is implicated in amyotrophic lateral sclerosis (ALS), and some hereditary mutations localized in the low complexity domain (LCD) facilitate the formation of pathogenic TDP-43 fibrils. A recent cryo-EM study reported the atomic-level structures of the A315E TDP-43 LCD (residues 288-319, TDP-43_288-319) core fibril in which the protofilaments have R-shaped structures and hypothesized that A315E U-shaped protofilaments can readily convert to R-shaped protofilaments compared to the wild-type (WT) ones. There are no atomic structures of WT protofilaments available yet. Herein, we performed extensive all-atom explicit-solvent molecular dynamics simulations on A315E and WT protofilaments starting from both the cryo-EM-determined R-shaped and our constructed U-shaped structures. Our simulations show that WT protofilaments also adopt the R-shaped structures but are less stable than their A315E counterparts. Except for R293-E315 salt bridges, N312-F316 hydrophobic interactions and F316-F316 π-π stacking interactions are also crucial for the stabilization of the neck region of the R-shaped A315E protofilaments. The loss of R293-E315 salt bridges and the weakened interactions of N312-F316 and F316-F316 result in the reduced stability of the R-shaped WT protofilaments. Simulations starting from U-shaped folds reveal that A315E protofilaments can spontaneously convert to the cryo-EM-derived R-shaped protofilaments, whereas WT protofilaments convert to R-shape-like structures with remodeled neck regions. The R-shape-like WT protofilaments could act as intermediate states slowing down the U-to-R transition. This study reveals that A315E mutation can not only enhance the structural stability of the R-shaped TDP-43_288-319 protofilaments but also promote the U-to-R transition, which provides atomistic insights into the A315E mutation-enhanced TDP-43 pathogenicity in ALS.

Stable Cavitation Interferes with Aβ16-22 Oligomerization

Ultrasound and microbubbles are used for many medical applications nowadays. Scanning ultrasound can remove amyloid-β (Aβ) aggregates in the mouse brain and restores memory in an Alzheimer's disease mouse model. In vitro studies showed that amyloid fibrils are fragmented due to the ultrasound-induced bubble inertial cavitation, and ultrasonic pulses accelerate the depolymerization of Aβ fibrils into monomers at 1 μM of concentration. Under applied ultrasound, microbubbles can be in a stable oscillating state or unstable inertial cavitation state. The latter occurs when ultrasound causes a dramatic change of bubble sizes above a certain acoustic pressure. We have developed and implemented a nonequilibrium molecular dynamics simulation algorithm to the AMBER package, to facilitate the investigation of the molecular mechanism of Aβ oligomerization under stable cavitation. Our results indicated that stable cavitation not only inhibited oligomeric formation, but also prevented the formation of β-rich oligomers. The network analysis of state transitions revealed that stable cavitation altered the oligomerization pathways of Aβ_16-22 peptides. Our simulation tool may be applied to optimize the experimental conditions to achieve the best therapeutical effect.

Deciphering the Role of ATP on PHF6 Aggregation

The aggregation of Tau protein, which are involved in Alzheimer's disease, are associated with the self-assembly of the hexapeptide sequence, paired helical filament 6 (PHF6) from repeat 3 of Tau. In order to treat Alzheimer's disease and other such tauopathies, one of the therapeutic strategies is to inhibit aggregation of Tau and its nucleating segments. Therefore, we have studied the effect of adenosine triphosphate (ATP) on the aggregation of PHF6. ATP has, interestingly, demonstrated its ability to inhibit and dissolve protein aggregates. Using classical molecular dynamics simulations, we observed that the hydrophobic core of PHF6 segment displays extended β-sheet conformation, which stabilizes PHF6 aggregates. However, the distribution of ATP around the vicinity of the peptides enables PHF6 to remain discrete and attain random coil conformers. The interpeptide interactions are substituted by PHF6-ATP interactions through hydrogen bonding and hydrophobic interactions (including π-π stacking). Furthermore, the adenosine moiety of ATP contributes more than the triphosphate chain toward PHF6-ATP interaction. Ultimately, this work establishes the inhibitory activity of ATP against Tau aggregation; hence, the therapeutic effect of ATP should be explored further in regard to the effective treatment of Alzheimer's disease.

Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain

Fused in sarcoma (FUS), a nuclear RNA binding protein, can not only undergo liquid-liquid phase separation (LLPS) to form dynamic biomolecular condensates but also aggregate into solid amyloid fibrils which are associated with the pathology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration diseases. Phosphorylation in the FUS low-complexity domain (FUS-LC) inhibits FUS LLPS and aggregation. However, it remains largely elusive what are the underlying atomistic mechanisms of this inhibitory effect and whether phosphorylation can disrupt preformed FUS fibrils, reversing the FUS gel/solid phase toward the liquid phase. Herein, we systematically investigate the impacts of phosphorylation on the conformational ensemble of the FUS_37-97 monomer and dimer and the structure of the FUS_37-97 fibril by performing extensive all-atom molecular dynamics simulations. Our simulations reveal three key findings: (1) phosphorylation shifts the conformations of FUS_37-97 from the β-rich, fibril-competent state toward a helix-rich, fibril-incompetent state; (2) phosphorylation significantly weakens protein-protein interactions and enhances protein-water interactions, which disfavor FUS-LC LLPS as well as aggregation and facilitate the dissolution of the preformed FUS-LC fibril; and (3) the FUS_37-97 peptide displays a high β-strand probability in the region spanning residues 52-67, and phosphorylation at S54 and S61 residues located in this region is crucial for the disruption of LLPS and aggregation of FUS-LC. This study may pave the way for ameliorating phase-separation-related pathologies via site-specific phosphorylation.

Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide-Peptide and Peptide-Solvent Interactions

Atomic descriptions of peptide self-assembly are crucial to an understanding of disease-related peptide aggregation and the design of peptide-assembled materials. Obtaining these descriptions through computer simulation is challenging because current force fields, which were not designed for this process and are often unable to describe correctly peptide self-assembly behavior and the sequence dependence. Here, we developed a framework using dipeptide aggregation as a model system to improve force fields for simulations of self-assembly. Aggregation-related structural properties were designed and used to guide the optimization of peptide-peptide and peptide-solvent interactions. With this framework, we developed a self-assembly force field, termed PACE-ASM, by reoptimizing a hybrid-resolution force field that was originally developed for folding simulation. With its applicability in folding simulations, the new PACE was used to simulate the self-assembly of two disease-related short peptides, Aβ_16-21 and PHF6, into β-sheet-rich cross-β amyloids. These simulations reproduced the crystal structures of Aβ_16-21 and PHF6 amyloids at near-atomic resolution and captured the difference in packing orientations between the two sequences, a task which is challenging even with all-atom force fields. Apart from cross-β amyloids, the self-assembly of emerging helix-rich cross-α amyloids by another peptide PSMα3 can also be correctly described with the new PACE, manifesting the versatility of the force field. We demonstrated that the ability of the PACE-ASM to model peptide self-assembly is based largely on its improved description of peptide-peptide and peptide-solvent interactions. This was achieved with our optimization framework that can readily identify and address the deficiency in describing these interactions.

Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces

Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.

Protein assembly and crowding simulations

Proteins encounter frequent molecular interactions in biological environments. Computer simulations have become an increasingly important tool in providing mechanistic insights into how such interactions in vivo relate to their biological function. The review here focuses on simulations describing protein assembly and molecular crowding effects as two important aspects that are distinguished mainly by how specific and long-lived protein contacts are. On the topic of crowding, recent simulations have provided new insights into how crowding affects protein folding and stability, modulates enzyme activity, and affects diffusive properties. Recent studies of assembly processes focus on assembly pathways, especially for virus capsids, amyloid aggregation pathways, and the role of multivalent interactions leading to phase separation. Also, discussed are technical challenges in achieving increasingly realistic simulations of interactions in cellular environments.

Joint Computational/Cell-Based Approach for Screening Inhibitors of Tau Oligomerization: A Proof-of-Concept Study

BACKGROUND

Tau assembly produces soluble oligomers and insoluble neurofibrillary tangles, which are neurotoxic to the brain and associated with Alzheimer's and Parkinson's diseases. Therefore, preventing tau aggregation is a promising therapy for those neurodegenerative disorders.

OBJECTIVE

The aim of this study was to develop a joint computational/cell-based oligomerization protocol for screening inhibitors of tau assembly.

METHODS

Virtual oligomerization inhibition (VOI) experiment using molecular dynamics simulation was performed to screen potential oligomerization inhibitors of PHF6 hexapeptide. Tau seeding assay, which is directly related to the outcome of therapeutic intervention, was carried out to confirm a ligand's ability in inhibiting tau assembly formation.

RESULTS

Our protocol was tested on two known compounds, EGCG and Blarcamesine. EGCG inhibited both the aggregation of PHF6 peptide in VOI and tau assembly in tau seeding assay, while Blarcamesine was not a good inhibitor at the two tasks. We also pointed out that good binding affinity to tau aggregates is needed, but not sufficient for a ligand to become a good inhibitor of tau oligomerization.

CONCLUSION

VOI goes beyond traditional computational inhibitor screening of amyloid aggregation by directly examining the inhibitory ability of a ligand to tau oligomerization. Comparing with the traditional biochemical assays, tau seeding activities in cells is a better indicator for the outcome of a therapeutic intervention. Our hybrid protocol has been successfully validated. It can effectively and efficiently identify the inhibitors of amyloid oligomerization/aggregation processes, thus, facilitate to the drug development of tau-related neurodegenerative diseases.