Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.

Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril

Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.

The Role of Chloride ion in the Silicate Condensation Reaction from ab Initio Molecular Dynamics Simulations

The comprehension of silicate oligomer formation during the initial stage of zeolite synthesis is of significant importance. In this study, we investigated the effect of chloride ions (Cl-) on silicate oligomerization using ab initio molecular dynamics simulations with explicit water molecules. The results show that the presence of Cl- increases the free energy barriers of all reactions compared to the case without the anion. The formation of the 4-ring structure has the lowest free energy barrier (73 kJ/mol), while the formation of the 3-ring structure has the highest barrier (98 kJ/mol) in the presence of Cl-. These findings suggest that Cl- suppresses the formation of 3-rings and favors the formation of larger oligomers in the process of zeolite synthesis. Our study provides important insights into the directing role of Cl- in silicate oligomerization by regulating thermodynamic and kinetic parameters. An important point to consider is the impact of the anion on aqueous reactions, particularly in altering the hydrogen bond network around reactive species. These results also provide a basis for further studies of the formations of larger silicate oligomers in solution.

Histidine tautomerism-mediated transthyretin amyloidogenesis: A molecular insight

Characterization of the conformational alterations involved in monomer misfolding is essential for elucidating the molecular basis of the initial stage of protein accumulation. Here, we report the first structural analyses of transthyretin (TTR) (26-57) fragments with two histidine tautomeric states (δ; N_δ1H and ε; N_ε2H) using replica-exchange molecular dynamics (REMD) simulations. Explaining the organizational properties and misfolding procedure is challenging because the δ and ε configurations can occur in the free neutral state. REMD revealed that β-sheet generation is favored for the δδ (16.8%) and εδ (6.7%) tautomeric isomers, showing frequent main-chain contacts between the stable regions near the head (N-terminus) and central (middle) part compared to the εε (4.8%) and δε (2.8%) isomers. The presence of smaller and wider local energy minima may be related to the structural stability and toxicity of δδ/εδ and εε/δε. Histidines31 and 56 were the parts of regular (such as β-strand) and nonregular (such as coil) secondary structures within the highly toxic TTR isomer. For TTR amyloidosis, focusing on hazardous isomeric forms with high sheet contents may be a potent treatment strategy. Overall, our findings support the tautomerism concept and aid in our comprehension of the basic tautomeric actions of neutral histidine throughout the misfolding process.

Insight into the role of excess hydroxide ions in silicate condensation reactions

The formation of silicate oligomers in the early stages is key to zeolite synthesis. The pH and the presence of hydroxide ions are important in regulating the reaction rate and the dominant species in solutions. This paper describes the formation of silicate species, from dimers to 4-membered rings, using ab initio molecular dynamics simulations in explicit water molecules with an excess hydroxide ion. The thermodynamic integration method was used to calculate the free energy profile of the condensation reactions. The hydroxide group's role is not only to control the pH of the environment, but also to actively participate in the condensation reaction. The results show that the most favorable reactions are linear-tetramer and 4-membered-ring formation, with overall barriers of 71 kJ mol^-1 and 73 kJ mol^-1, respectively. The formation of trimeric silicate, with the largest free-energy barrier of 102 kJ mol^-1, is the rate-limiting step under these conditions. The excess hydroxide ion aids in the stabilization of the 4-membered-ring structure over the 3-membered-ring structure. Due to a relatively high free-energy barrier, the 4-membered ring is the most difficult of the small silicate structures to dissolve in the backward reaction. This study is consistent with the experimental observation that silicate growth in zeolite synthesis is slower in a very-high-pH environment.

New Insights into the Structural and Binding Properties on Aβ Mature Fibrils Due to Histidine Protonation Behaviors

Histidine tautomeric behaviors have been considered origin factors for controlling the structure and aggregation properties of misfolding peptides. Except for tautomeric behaviors, histidine protonation behaviors definitely have the same capacities due to the net charge changes and the various N/N-H orientations on imidazole rings. However, such phenomena are still unknown. In the current study, Aβ mature fibrils substituted with various protonation states were performed by molecular dynamics simulations to investigate the structure and binding properties. Our results show that all kinds of protonation states can increase the ΔG1 stability and decrease ΔG2 and ΔG3 stabilities. A significantly higher averaged β-sheet content was detected in (εεp), (εpp), and (ppp) fibrils in one, two, and three protonation stages, respectively. Impressively, we found that the substituted fibril with specific protonated states can control the N-terminus structural properties. Further analysis confirmed that H6 and H13 are more important than H14 since the H-bond donor and receptor cooperate among C1/C3/C8_H6, C1/C3/C8_H13, and C1/C3/C8_E11. Furthermore, the mechanism of protonation behaviors was discussed. The current study is helpful for understanding the histidine protonation behaviors on one, two, and three protonation stages, which provides new horizons for exploring the origin of protein folding and misfolding.

Structural properties of Aβ (1-40) peptide in protonation stage of one, two, and three: New insights from the histidine protonation behaviors

Structural properties and aggregation tendency can be significantly influenced by histidine behaviors (histidine on N^δ-H state is defined as δ, likewise, N^ε-H: ε and both N^δ-H and N^ε-H: p). In current study, we investigated structural properties of Aβ(1-40) peptide during protonation evolution stage of one, two, and three by total 19 independent replica exchange molecular dynamics simulations using implicit solvent. Our results show that any kind of protonated state will promote β-sheet structure formation in comparison with deprotonated (εεε). With increase in number of protonation, the lowest β-sheet content increased. The highest averaged β-sheet structure content was detected in (δpδ) (46.0 %), (εpp) (36.8 %), and (ppp) (16.0 %) in each protonation stage. With three β-strand structures, (δpδ) shows more stable features and high hydrophobic properties. Further analysis confirmed that H13 and H14 are more important than H6. Specifically, H13 and H14 have a synergistic effect for structural formations by controlling H-bond networks in H13(p) with V39/V40 and H14(p/δ) with G37/G38. Finally, the Pearson correlation coefficient results confirmed that experimental result (ref. 44) is corresponding to our (εpp) system. Our current study will be conducive to understanding the effects of the histidine behaviors, it provides new insights for exploration protein folding and misfolding processes.

Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation

Intrinsically disordered peptides, such as amyloid β42 (Aβ42), lack a well-defined structure in solution. Aβ42 can undergo abnormal aggregation and amyloidogenesis in the brain, forming fibrillar plaques, a hallmark of Alzheimer's disease. The insoluble fibrillar forms of Aβ42 exhibit well-defined, cross β-sheet structures at the molecular level and are less toxic than the soluble, intermediate disordered oligomeric forms. However, the mechanism of initial interaction of monomers and subsequent oligomerization is not well understood. The structural disorder of Aβ42 adds to the challenges of determining the structural properties of its monomers, making it difficult to understand the underlying molecular mechanism of pathogenic aggregation. Certain regions of Aβ42 are known to exhibit helical propensity in different physiological conditions. NMR spectroscopy has shown that the Aβ42 monomer at lower pH can adopt an α-helical conformation and as the pH is increased, the peptide switches to β-sheet conformation and aggregation occurs. CD spectroscopy studies of aggregation have shown the presence of an initial spike in the amount of α-helical content at the start of aggregation. Such an increase in α-helical content suggests a mechanism wherein the peptide can expose critical non-polar residues for interaction, leading to hydrophobic aggregation with other interacting peptides. We have used molecular dynamics simulations to characterize in detail the conformational landscape of monomeric Aβ42 in solution to identify molecular properties that may mediate the early stages of oligomerization. We hypothesized that conformations with α-helical structure have a higher probability of initiating aggregation because they increase the hydrophobicity of the peptide. Although random coil conformations were found to be the most dominant, as expected, α-helical conformations are thermodynamically accessible, more so than β-sheet conformations. Importantly, for the first time α-helical conformations are observed to increase the exposure of aromatic and hydrophobic residues to the aqueous solvent, favoring their hydrophobically driven interaction with other monomers to initiate aggregation. These findings constitute a first step toward characterizing the mechanism of formation of disordered, low-order oligomers of Aβ42.

Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N-H and C-H cleavages

The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60 kcal mol^-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.

Histidine tautomerism dependent conformational transitions driven aggregation of profilin-1: Implications in amyotrophic lateral sclerosis

Aggregation of profilin-1 (PFN1) causes a fatal neurodegenerative disease, familial amyotrophic lateral sclerosis (fALS). Histidine (His) tautomerism has been linked to the formation of fibril aggregation causing neurodegenerative disease. Characterization of intermediate species that form during aggregation is crucial, however, this has proven very challenging for experimentalists due to their transient nature. Hence, molecular dynamics (MD) simulations have been performed on the His tautomeric isomers εε, εδ, δε, and δδ of PFN1 to explain the structural changes and to correlate them with its aggregation propensity. MD simulations show that His133 presumably plays a major role in the aggregation of PFN1 upon His tautomerism compared to His119. Further, the formation of a new 3₁₀-helix is observed in εε and δε but 3₁₀-helix is not observed in δδ and εδ isomers. In addition, our findings unveil that β-sheet dominating conformations are observed in His119(δ)-His133(δ) δδ isomer of PFN1 with significant antiparallel β-sheets between residues T15-G23, S29-A33, L63-L65, Q68-S76, F83-T89, T97-T105, and K107-K115, suggesting a novel aggregation mechanism possibly occur for the formation of PFN1 aggregates. Overall, these results propose that MD simulations of PFN1 His tautomers can provide a detailed microscopic understanding of the aggregation mechanisms which are hard to probe through experiments.

Reaction Mechanisms of Histidine and Carnosine with Hypochlorous Acid Along with Chlorination Reactivity of N-Chlorinated Intermediates: A Computational Study

Hypochlorous acid (HOCl) released from activated leukocytes not only plays a significant role in the human immune system but is also implicated in numerous diseases including atherosclerosis and some cancers due to its inappropriate production. Histidine (His) and carnosine (Car), as a respective mediator and protective agent of HOCl damage, have attracted considerable attention; however, their detailed reaction mechanisms are still unclear. In this study, using a His residue with two peptide bond groups (HisRes) as a model, the reaction mechanisms of HisRes and Car including N_εH and N_δH tautomers with HOCl along with the chlorination reactivity of N-chlorinated intermediates were investigated by quantum chemical methods. The obtained results indicate that in the imidazole side chain, the pyridine-like N is the most reactive site rather than the pyrrole-like N, and the kinetic order of all of the possible reaction sites in HisRes follows pyridine-like N > imidazole C_δ ≫ imidazole C_ε > pyrrole-like N, while that in Car is pyridine-like N ≫ imidazole C_δ ≫ amide N. As for N-chlorinated intermediates at imidazole, although the unprotonated form has a low chlorination reactivity as expected, it can still chlorinate tyrosine. Especially, the protonated form exhibits similar ability to HOCl, causing secondary damage in vivo. N-Chlorinated Car features higher internal chlorine migration ability than its intermolecular transchlorination, preventing further HOCl-induced damage. Additionally, a generally overlooked nucleophilic Cl^- shift is also found in N-chlorinated Car/HisRes, indicating that nucleophilic sites in biomolecules also need to be considered. The outcomes of this study are expected to expand our understanding of secondary damage and protective mechanisms involved in HOCl in humans.

Mechanistic Insights into the Polymorphic Associations and Cross-Seeding of Aβ and hIAPP in the Presence of Histidine Tautomerism: An All-Atom Molecular Dynamic Study

Hundreds of millions of people around the world have been affected by Type 2 diabetes (T2D) which is a metabolic disorder. Clinical research has revealed T2D as a possible risk factor for Alzheimer's disease (AD) development (and vice versa). Amyloid-β (Aβ) and human islet amyloid polypeptide are the main pathological species in AD and T2D, respectively. However, the mechanisms by which these two amyloidogenic peptides co-aggregate are largely uninvestigated. Herein, for the first time, we present the cross-seeding between Amylin1-37 and Aβ40 considering the particular effect of the histidine tautomerism at atomic resolution applying the all-atom molecular dynamics (MD) simulations for heterodimeric complexes. The results via random seed MD simulations indicated that the Aβ40(δδδ) isomer in cross-talking with Islet(ε) and Islet(δ) isomers could retain or increase the β-sheet content in its structure that may make it more prone to further aggregation and exhibit higher toxicity. The other tautomeric isomers which initially did not have a β-sheet structure in their monomeric forms did not show any generated β-sheet, except for one seed of the Islet(ε) and Aβ40(εεε) heterodimers complex that displayed a small amount of formed β-sheet. This computational research may provide a different point of view to examine all possible parameters that may contribute to the development of AD and T2D and provide a better understanding of the pathological link between these two severe diseases.

Theoretical Insights into Mutation and Histidine Tautomerism Effects on Tau Proteins

Research on misfolding of tau proteins will help to better understand the formation process of neurofibrillary tangles, a hallmark of Alzheimer's disease. Mutation and histidine tautomeric effects have been considered the two most important inherent factors for tau protein misfolding. In current research, replica-exchange molecular dynamics (REMD) were performed to characterize the structural properties of the key fragment R3 of tau protein under the collective effects of P332L mutation and histidine tautomerism. Simulation results suggest that though the content β-sheet of P332L R3 εδ isomer is slightly lower than that of the WT P332L R3 fragment, the total stable secondary structures including β-sheet and helix of P332L R3 isomers are generally more prevalent than those of wild type R3, which may be the reason that P332L R3 has a higher aggregation tendency. Further analysis showed that the hydrogen bond networks are affected by the mutation and histidine tautomerism. Furthermore, the interactions between N-terminus and C-terminus play a crucial role in β-hairpin formation in all isomers. The current study will contribute to revealing the collective effects of P332L and histidine tautomerism on the misfolding of tau proteins.

Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective

The aggregation and structural conversion of normal prion peptide (PrP^C) into the pathogenic scrapie form (PrP^Sc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [N_ε2-H (ε) and N_δ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.

Role of the English (H6R) Mutation on the Structural Properties of Aβ40 and Aβ42 Owing to the Histidine Tautomeric Effect

As an intrinsic origin cause, histidine behaviors play a critical role in protein misfolding processes. Generally, the English (H6R) mutation will disrupt H6 interactions. However, the structural properties of Aβ40 H6R and Aβ42 H6R under the complex influence of a histidine tautomeric effect and an H6R mutation remain unclear. Therefore, we performed a replica exchange molecular dynamics simulation to unveil such structural properties. Our result showed that the H6R substitute could promote the generation of β-sheet structures in comparison to the wild type. Three β-strand structure properties were observed in Aβ40 (rδδ), Aβ42 (rεε), Aβ42 (rεδ), and Aβ42 (rδδ) with β-sheet contents of 47.5%, 37.2%, 46.9%, and 38.6%, respectively, and the dominant conformational properties of Aβ40 (rδδ), Aβ42 (rεε), Aβ42 (rεδ), and Aβ42 (rδδ) had top conformational states of 86.0%, 73.2%, 67.0%, and 56.5%, respectively. Further analysis confirmed that R6 had different mechanisms for controlling the conformational features in Aβ40 H6R and Aβ42 H6R. In the Aβ40 systems, H14 H-bond networks played a critical role in controlling the structural properties. However, in the Aβ42 systems, R6 was more important because it was directly involved in the β-strand formation and maintained the β-sheet between the N-terminus and the central hydrophobic core region. Our current study helps to elucidate the histidine tautomeric behaviors in H6R mutations, which will present opportunities to understand the correlation between with/without H6 and the Aβ40/Aβ42 H6R misfolding mechanisms.

Histidine Tautomerism Driving Human Islet Amyloid Polypeptide Aggregation in the Early Stages of Diabetes Mellitus Progression: Insight at the Atomistic Level

Early oligomerization of human islet amyloid polypeptide (hIAPP), which is accountable for β-cell death, has been implicated in the progression of type 2 diabetes mellitus. Some researches have shown the connection between hIAPP and Alzheimer's disease as well. However, the mechanism of peptide accumulation and associated cytotoxicity remains unclear. Due to the unique properties and significant role of histidine in protein sequences, here for the first time, the tautomeric effect of histidine at the early stages of amylin misfolding was investigated via molecular dynamics simulations. Considering Tau and Pi tautomeric forms of histidine (Tau and Pi tautomers are denoted as ϵ and δ, respectively), simulations were performed on two possible isomers of amylin. Our analysis revealed a higher probability of transient α-helix generation in the δ isomer in monomeric form. In dimeric forms, the δδ and δϵ conformations showed an elevated amount of α-helix and lower coil in comparison to the ϵϵ dimer. Due to the significant role of α-helix in membrane disruption and transition to β-sheet structure, these results may imply a noticeable contribution of the δ isomer and the δδ and δϵ dimers rather than ϵ and ϵϵ conformations in the early stages of diabetes initiation. Our results may aid in elucidating the hIAPP self-association process in the etiology of amyloidosis.

Molecular insight into the early stage of amyloid-β(1-42) Homodimers aggregation influenced by histidine tautomerism

Aggregated amyloid β-peptide (Aβ) in small oligomeric forms inside the brain causes synaptic function disruption and the development of Alzheimer's disease (AD). Histidine is an important amino acid that may lead to structural changes. Aβ42 monomer chain includes 3 histidine residues that considering two ε and δ tautomers 8 isomers, including (εεε) and (εδδ) could be formed. Molecular dynamics simulation on homodimerization of (εεε) (the most common type of tautomers) and (εδδ) tautomers with different initial configurations using monomer chains from our previous work were performed to uncover the tautomeric behavior of histidine on Aβ42 aggregation in a physiological pH which is still largely unknown and impossible to observe experimentally. We found a higher propensity of forming β-sheet in (εδδ) homodimers and specifically in a greater amount from Aβ42 than from Aβ40. A smaller amount of β-sheet formation was observed for (εεε) homodimers compared with (εδδ). Additionally, interactions in (εδδ) homodimers may indicate the importance of the hydrophobic core and C-/N-terminals during oligomerization. Our findings indicate the important role of the tautomeric effect of histidine and (εδδ) homodimers at the early stage of Aβ aggregation.

Histidine Tautomeric Effect on the Key Fragment R3 of Tau Protein from Atomistic Simulations

Self-assembly of hyperphosphorylated tau proteins into neurofibrillary tangles (NFT) is a hallmark of Alzheimer's disease. Previous studies suggest that the tau monomer may play an important role in NFTs formation in two general categories: inert (M_i) monomer and seed-competent (M_s) monomer. In the current study, replica-exchange molecular dynamics (REMD) were performed to investigate the effect of histidine tautomerism on the structures of a key fragment (R3) of tau protein and the transformation between different conformations. Based on the simulation results, we propose the histidine tautomerism hypothesis for tau protein misfolding. Histidine tautomerism greatly expands the conformational library, which triggers the emergence of conformations with higher aggregation tendency. Moreover, the conversions existing in both isomers and conformations may cause protein misfolding to occur more readily.

Small-Molecule Targeted Aβ42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones

Heavy evidence has confirmed that Aβ42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aβ42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-β peptide Aβ42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aβ and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aβ42 and Aβ40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aβ42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aβ40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aβ40 oligomer. The HSA distinction between Aβ42 and Aβ40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (β1) and C-terminal (β2) regions of Aβ42 peptide, two key nucleation regions for Aβ intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aβ42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aβ aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aβ aggregates.

Molecular mechanism of amyloidogenicity and neurotoxicity of a pro-aggregated tau mutant in the presence of histidine tautomerism via replica-exchange simulation

Considering ΔK280 tau mutation, δε isomer with highest sheet content may accelerate aggregation; generating small compounds to inhibit this would help tp prevent tauopathies.

Intrinsic Origin of Tau Protein Aggregation: Effects of Histidine Tautomerism on Tau267-312 Monomer

Histidine tautomerism is considered a crucial component that affects the constitutional and accumulation characteristics of the tau_267-312 monomer in the neutral condition, which are connected with the pathobiology of Alzheimer's disease (AD). Interpreting the organizational characteristics and accumulation procedure is a challenging task because two tautomeric conformations (the N^ε-H or N^δ-H tautomer) can occur in the open neutral condition. In the current work, replica-exchange molecular dynamics (REMD) simulations were performed to investigate the structural properties of the tau_267-312 monomer considering the histidine tautomeric effect. Based on the simulation outcomes, the histidine 268 (H268) (δ)-H299 (δ) (δδ) isomer had the highest β-sheet content with a value of 26.2%, which acquires a sheet-governing toxic conformer with the first abundant conformational state of 22.6%. In addition, δδ displayed notable antiparallel β-sheets between lysine 8 (K8)-asparagine 13 (N13) and valine 40 (V40)-tyrosine 44 (Y44) as well as between K32-H33 and V40-Y44 (β-meander supersecondary structure), indicating this tautomeric isomer may exist to stimulate tau oligomerization. Furthermore, H299 was found to play an essential role in the structural stabilization of the δδ isomer compared with H268. The present research will aid in obtaining insight into the organizational and accumulation properties of tau protein in the presence of histidine tautomerism to control AD.

Elucidating the Role of Tetraethylammonium in the Silicate Condensation Reaction from Ab Initio Molecular Dynamics Simulations

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is important. The use of organic structure-directing agents (OSDAs) is known to be a key factor in the formation of different silicate species and the final zeolite structure. For example, tetraethylammonium ion (TEA⁺) is a commonly used organic template for zeolite synthesis. In this study, ab initio molecular dynamics (AIMD) simulation is used to provide an understanding of the role of TEA⁺ in the formation of various silicate oligomers, ranging from dimer to 4-ring. Calculated free-energy profiles of the reaction pathways show that the formation of a 4-ring structure has the highest energy barrier (97 kJ/mol). The formation of smaller oligomers such as dimer, trimer, and 3-ring has lower activation barriers. The TEA⁺ ion plays an important role in regulating the predominant species in solution via its coordination with silicate structures during the condensation process. The kinetics and thermodynamics of the oligomerization reaction indicate a more favorable formation of the 3-ring over the 4-ring structure. The results from AIMD simulations are in line with the experimental observation that TEA⁺ favors the 3-ring and double 3-ring in solution. The results of this study imply that the role of OSDAs is not only important for the host-guest interaction but also crucial for controlling the reactivity of different silicate oligomers during the initial stage of zeolite formation.

Impact of A2V Mutation and Histidine Tautomerism on Aβ42 Monomer Structures from Atomistic Simulations

The self-assembly of amyloid-β (Aβ) peptides into senile plaques in the brain is a hallmark of Alzheimer's disease (AD) pathology. Mutation and histidine tautomerism are considered intrinsic origins in the accumulation of Aβ. As a first step toward understanding the impact of A2V mutation and histidine tautomerism on the Aβ42 isoform, we performed replica-exchange molecular dynamics (REMD) simulations to investigate the effects of histidine tautomerism on the structural properties of A2V Aβ42 peptides. There are generally more β-sheet and less α-helix secondary structures in A2V Aβ42 monomers than in WT Aβ42, implying a higher aggregation tendency in A2V Aβ42, which is consistent with previous studies. The current research will help develop the histidine tautomerism hypothesis of misfolded protein aggregation and eventually elucidate the pathogenesis of AD.

First-Principles Calculation of Water pKa Using the Newly Developed SCAN Functional

Acid/base chemistry is an intriguing topic that still constitutes a challenge for computational chemistry. While estimating the acid dissociation constant (or pK_a) could shed light on many chemistry processes, especially in the fields of biochemistry and geochemistry, evaluating the relative stability between protonated and nonprotonated species is often very difficult. Indeed, a prerequisite for calculating the pK_a of any molecule is an accurate description of the energetics of water dissociation. Here, we applied constrained molecular dynamics simulations, a noncanonical sampling technique, to investigate the water deprotonation process by selecting the OH distance as the reaction coordinate. The calculation is based on density functional theory and the newly developed SCAN functional, which has shown excellent performance in describing water structure. This first benchmark of SCAN on a chemical reaction shows that this functional accurately models the energetics of proton transfer reactions in an aqueous environment. After taking Coulomb long-range corrections and nuclear quantum effects into account, the estimated water pK_a is only 1.0 pK_a unit different from the target experimental value. Our results show that the combination of SCAN and constrained MD successfully reproduces the chemistry of water and constitutes a good framework for calculating the free energy of chemical reactions of interest.

Intrinsic Origin of Amyloid Aggregation: Collective Effects of the Mutation and Tautomerism of Histidine

Mutation is considered an important factor in the accumulation of amyloid-β (Aβ), which is a hallmark of Alzheimer's disease (AD). A2V Aβ40 shows a higher aggregation tendency; however, the existing knowledge is not sufficient to explain the mechanism. We performed replica-exchange molecular dynamics simulations (REMD) to investigate the structural properties of A2V Aβ40 monomers and consider the tautomerism of histidine. The collective effects of the mutation and tautomerism leads A2V Aβ40 to much higher β-sheet and lower α-helix contents than WT Aβ40, which may explain the enhanced aggregation kinetics of A2V Aβ40 with respect to WT Aβ40. The current research provides new insights on understanding the pathology of AD.

Structural and Binding Properties on Aβ Mature Fibrils Due to the Histidine Tautomeric Effect

Many studies have focused on histidine behaviors in misfolding diseases. However, histidine behaviors on mature fibrils are still unknown. In the current study, we investigated mature fibrils with various histidine states to understand the structural properties of the histidine tautomeric effect on mature fibrils. Our results show that substituting chain 1 with different histidine states affects Aβ structural properties in A2, D7-G9, H14-Q15, S26-N27, and G33-G37 regions. The binding free energies with substituted fibrils were influenced not only along the axial direction, but also between duplex fibrils. Our results suggest that substituted (εδδ) preferentially disturbed the stability among the current mature fibrils. Further, H-bonded network differences indicate that twisted morphologies in mature fibrils are derived from the position and orientation of the imidazole ring in histidines. Our current study helps to elucidate histidine behaviors on mature fibrils, which will present opportunities to understand the misfolding mechanisms.

Tautomerization Effect of Histidines on Oligomer Aggregation of β-Amyloid(1-40/42) during the Early Stage: Tautomerism Hypothesis for Misfolding Protein Aggregation

As the intrinsic origin of the hypothesis for β-amyloid (Aβ) from Alzheimer's disease, histidine behaviors were found to play a crucial role in Aβ aggregation. To investigate the histidine behaviors during the early stage of aggregation, Aβ40/42 pentamers with different histidine isomer states were simulated at the atomic level. Results show that five Aβ40 (δδδ) and Aβ42 (εδδ) monomers can rapidly decrease the aggregation threshold, promote stable pentamer formation, and increase pentamer contents by 51.8% and 56.7%, respectively, as compared with the values of their wild-type (εεε) counterparts. Additionally, pentamers of Aβ40 (δδδ) and Aβ42 (εδδ) have different aggregation pathways and disassembly species, Tr+D and Te+M, during the growth of the pentamer. This work discloses the significance of histidine tautomerization in Aβ aggregation, implying a potential way to control Aβ aggregation and develop the assembly inhibitors.

Tautomeric Effect of Histidine on the Monomeric Structure of Amyloid β-Peptide(1-42)

Tautomeric state of histidine is one of the factors that influence the structural and aggregation properties of amyloid β (Aβ)-peptide in neutral state. It is worth it to uncover the monomeric properties of Aβ(1-42) peptide in comparison with Aβ(1-40) peptide. Our replica-exchange molecular dynamics simulations results show that the sheet content of each tautomeric isomer in Aβ(1-42) monomer is slightly higher than that in Aβ(1-40) monomer except His6(δ)-His13(δ)-His14(δ) (δδδ) isomer, implying higher aggregation tendency in Aβ(1-42), which is in agreement with previous experimental and theoretical studies. Further analysis indicates that (εεε), (εδε), (εδδ), and (δδε) isomers prefer sheet conformation although they are in nondominating states. Particularly, it is confirmed that antiparallel β-sheets of (εδδ) were formed at K16-E22 (22.0-43.9%), N27-A30 except G29 (21.9-40.2%), and M35-I41 except G37 (24.1-43.4%). Furthermore, (εδδ) may be the easiest one to overcome structural transformation due to nonobstructing interactions between K16 and/or L17 and histidine residues. The current study will help to understand the tautomeric effect of Aβ(1-42) peptide to overcome Alzheimer's disease.

Theoretical study of deuterium isotope effects on acid–base equilibria under ambient and hydrothermal conditions

The calculated difference between pK_a values in H₂O and D₂O is in excellent agreement with experiment.

[UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations

X-Ray diffraction and Car–Parrinello molecular dynamics simulations furnish insights into the speciation of uranyl(vi) in liquid ammonia, calling special attention to the effect of solvation on the U–N bond length and bond strength.

The role of a structure directing agent tetramethylammonium template in the initial steps of silicate oligomerization in aqueous solution

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is of fundamental scientific and technological importance.

Proton release from the histidine-tetrad in the M2 channel of the influenza A virus

The activity of the M2 proton channel of the influenza A virus is controlled by pH. The tautomeric state and conformation of His37, a key residue in the M2 transmembrane four-helix bundle, controls the gating of the channel. Previously, we compared the energetics and dynamics of two alternative conformations of the doubly protonated state at neutral pH, namely, a 4-fold symmetric “histidine-box” and a 2-fold symmetric “dimer-of-dimers”, and proposed a multiconfiguration model for this charge state. Here, we elaborate this model by further studying configurations of the His37 tetrad in the triply protonated state and its subsequent deprotonation via quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, starting with the aforementioned configurations, to gain information about proton release in a viral membrane environment. Interestingly, the two configurations converge under acidic pH conditions. Protons can be transferred from one charged His37 to a neighboring water cluster at the C-terminal side of the channel when the Trp41 gate is open transiently. With limited backbone expansion, the free energy barrier for proton release to the viral interior at low pH is ∼6.5 kcal/mol in both models, which is much lower than at either neutral pH or for an isolated His37 cluster without a membrane environment. Our calculations also suggest that the M2 protein would seem to exclude the entrance of anions into the central channel through a special mechanism, due to the latter’s potential inhibitory effect on proton conduction.

Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation

Accurately calculating a weak acid's pK_a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK_a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK_a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK_a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton.

Predicting pKa in Implicit Solvents: Current Status and Future Directions

Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.

Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nε positions of the imidazole group to estimate the pKa's. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

The 3ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the DeltaG(bind) of the QPLD model perform much better than the RESP model, with the DeltaG(bind) estimation for QPLD model (-16.11 kcal/mol) versus DeltaG(bind) estimation for RESP model (-10.05 kcal/mol).

Ab Initio Molecular Dynamics Free-Energy Study of Microhydration Effects on the Neutral–Zwitterion Equilibrium of Phenylalanine

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.