Aggregates Sealed by Ions

The chapter draws a line connecting some recent results where the role of ions is found essential in sealing more or less pre-organized assemblies of macromolecules. We draw some dots along the line that starts from the effect of the ionic atmosphere and ends with the chemical bonds formed by multivalent ions acting as bridges between macromolecules. Many of these dots involve structurally disordered peptides and disordered regions of proteins. A broad perspective of the role of multivalent ions in assisting the assembly process, shifting population in polymorphic states, and sealing protein aggregates, is suggested.

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide's spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases

Amyloid-β (Aβ) and α-synuclein (αS) are two intrinsically disordered proteins (IDPs) at the centers of the pathogenesis of Alzheimer's and Parkinson's diseases, respectively. Different hypotheses have been proposed for explanation of the molecular mechanisms of the pathogenesis of these two diseases, with these two IDPs being involved in many of these hypotheses. Currently, we do not know, which of these hypothesis is more accurate. Experiments face challenges due to the rapid conformational changes, fast aggregation processes, solvent and paramagnetic effects in studying these two IDPs in detail. Furthermore, pathological modifications impact their structures and energetics. Theoretical studies using computational chemistry and computational biology have been utilized to understand the structures and energetics of Aβ and αS. In this chapter, we introduce Aβ and αS in light of various hypotheses, and discuss different experimental and theoretical techniques that are used to study these two proteins along with their weaknesses and strengths. We suggest that a promising solution for studying Aβ and αS at the center of varying hypotheses could be provided by developing new techniques that link quantum mechanics, statistical mechanics, thermodynamics, bioinformatics to machine learning. Such new developments could also lead to development in experimental techniques.

Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies

Monomers and oligomers of the amyloid-β peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition metal ions, affecting the mechanism and kinetics of amyloid-β aggregation. Due to the disordered nature of amyloid-β, its rapid aggregation, as well as solvent and paramagnetic effects, experimental studies face challenges in the characterization of transition metal ions bound to amyloid-β monomers and oligomers. The details of the coordination chemistry between transition metals and amyloid-β obtained from experiments remain debated. Furthermore, the impact of transition metal ion binding on the monomeric or oligomeric amyloid-β structures and dynamics are still poorly understood. Computational chemistry studies can serve as an important complement to experimental studies and can provide additional knowledge on the binding between amyloid-β and transition metal ions. Many research groups conducted first-principles calculations, ab initio molecular dynamics simulations, quantum mechanics/classical mechanics simulations, and classical molecular dynamics simulations for studying the interplay between transition metal ions and amyloid-β monomers and oligomers. This review summarizes the current understanding of transition metal interactions with amyloid-β obtained from computational chemistry studies. We also emphasize the current view of the coordination chemistry between transition metal ions and amyloid-β. This information represents an important foundation for future metal ion chelator and drug design studies aiming to combat Alzheimer's disease.

Selenium, selenoprotein P, and Alzheimer's disease: is there a link?

The essential trace element, selenium (Se), is crucial to the brain but it may be potentially neurotoxic, depending on dosage and speciation; Se has been discussed for decades in relation to Alzheimer's disease (AD). Selenoprotein P (SELENOP) is a secreted heparin-binding glycoprotein which serves as the main Se transport protein in mammals. In vivo studies showed that this protein might have additional functions such as a contribution to redox regulation. The current review focuses on recent research on the possible role of SELENOP in AD pathology, based on model and human studies. The review also briefly summarizes results of epidemiological studies on Se supplementation in relation to brain diseases, including PREADViSE, EVA, and AIBL. Although mainly positive effects of Se are assessed in this review, possible detrimental effects of Se supplementation or exposure, including potential neurotoxicity, are also mentioned. In relation to AD, various roles of SELENOP are discussed, i.e. as the means of Se delivery to neurons, as an antioxidant, in cytoskeleton assembly, in interaction with redox-active metals (copper, iron, and mercury) and with misfolded proteins (amyloid-beta and hyperphosphorylated tau-protein).

Different zinc(II) complex species and binding modes at Aβ N-terminus drive distinct long range cross-talks in the Aβ monomers

The present study addresses the reconstruction of the free-energy landscapes of amyloid-beta1-42 (Aβ42) coordinated respectively with one and two zinc ions, to scrutinize whether different Aβ-zinc complex species, i.e., mononuclear and dinuclear metal complexes, induce different Aβ conformation features. We found a subtle switch of intramolecular interactions, depending both on the zinc coordination environment and on the peptide to zinc stoichiometric ratio. On the one side, hairpin-like structures are predominant in mononuclear complexes, where a salt-bridge that involves Lys28-Glu22 and Lys16-Asp23 is stabilized. On the other side, elongated conformations are instead stabilized in the dinuclear zinc complexes. Experimental studies of atomic force microscopy as well as of zinc-Aβ complex species distribution diagrams provide evidence that the theoretical calculations can be rationalized in terms of the correlation between the increased amount of amorphous aggregates and the Aβ/Zn(2+) ratio.

Insights into the oxygen-based ligand of the low pH component of the Cu(2+)-amyloid-β complex

In spite of significant experimental effort dedicated to the study of Cu(2+) binding to the amyloid beta (Aβ) peptide, involved in Alzheimer's disease, the nature of the oxygen-based ligand in the low pH component of the Cu(2+)-Aβ(1-16) complex is still under debate. This study reports density-functional-theory-based calculations that explore the potential energy surface of Cu(2+) complexes including N and O ligands at the N-terminus of the Aβ peptide, with a focus on evaluating the role of Asp1 carboxylate in copper coordination. Model conformers including 3, 6, and 17 amino acids have been used to systematically study several aspects of the Cu(2+)-coordination such as the Asp1 side chain conformation, local peptide backbone geometry, electrostatic and/or hydrogen bond interactions, and number and availability of Cu(2+) ligands. Our results show that the Asp1 peptide carbonyl binds to Cu(2+) only if the coordination number is less than four. In contrast, if four ligands are available, the most stable structures include the Asp1 carboxylate in equatorial position instead of the Asp1 carbonyl group. The two lowest energy Cu(2+)-Aβ(1-17) models involve Asp1 COO(-), the N-terminus, and His6 and His14 as equatorial ligands, with either a carbonyl or a water molecule in the axial position. These models are in good agreement with experimental data reported for component I of the Cu(2+)-Aβ(1-16) complex, including EXAFS- and X-ray-derived Cu(2+)-ligand distances, Cu(2+) EPR parameters, and (14)N and (13)C superhyperfine couplings. Our results suggest that at low pH, Cu(2+)-Aβ species with Asp1 carboxylate equatorial coordination coexist with species coordinating the Asp1 carbonyl. Understanding the bonding mechanism in these species is relevant to gain a deeper insight on the molecular processes involving copper-amyloid-β complexes, such as aggregation and redox activity.

Identifying, by first-principles simulations, Cu[amyloid-β] species making Fenton-type reactions in Alzheimer's disease

According to the amyloid cascade hypothesis, amyloid-β peptides (Aβ) play a causative role in Alzheimer's disease (AD), of which oligomeric forms are proposed to be the most neurotoxic by provoking oxidative stress. Copper ions seem to play an important role as they are bound to Aβ in amyloid plaques, a hallmark of AD. Moreover, Cu-Aβ complexes are able to catalyze the production of hydrogen peroxide and hydroxyl radicals, and oligomeric Cu-Aβ was reported to be more reactive. The flexibility of the unstructured Aβ peptide leads to the formation of a multitude of different forms of both Cu(I) and Cu(II) complexes. This raised the question of the structure-function relationship. We address this question for the biologically relevant Fenton-type reaction. Computational models for the Cu-Aβ complex in monomeric and dimeric forms were built, and their redox behavior was analyzed together with their reactivity with peroxide. A set of 16 configurations of Cu-Aβ was studied and the configurations were classified into 3 groups: (A) configurations that evolve into a linearly bound and nonreactive Cu(I) coordination; (B) reactive configurations without large reorganization between the two Cu redox states; and (C) reactive configurations with an open structure in the Cu(I)-Aβ coordination, which have high water accessibility to Cu. All the structures that showed high reactivity with H2O2 (to form HO(•)) fall into class C. This means that within all the possible configurations, only some pools are able to produce efficiently the deleterious HO(•), while the other pools are more inert. The characteristics of highly reactive configurations consist of a N-Cu(I)-N coordination with an angle far from 180° and high water crowding at the open side. This allows the side-on entrance of H2O2 and its cleavage to form a hydroxyl radical. Interestingly, the reactive Cu(I)-Aβ states originated mostly from the dimeric starting models, in agreement with the higher reactivity of oligomers. Our study gives a rationale for the Fenton-type reactivity of Cu-Aβ and how dimeric Cu-Aβ could lead to a higher reactivity. This opens a new therapeutic angle of attack against Cu-Aβ-based reactive oxygen species production.

Effects of Zn2+ binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1 or Glu11?

Extensive experimental and computational studies have suggested that multiple Zn(2+) binding modes in amyloid β (Aβ) peptides could exist simultaneously. However, consistent results have not been obtained for the effects of Zn(2+) binding on Aβ structure, dynamics, and kinetics in particular. Some key questions such as why it is so difficult to distinguish the polymorphic states of metal ions binding to Aβ and what the underlying rationale is, necessitate elucidation. In this work, two 3N1O Zn(2+) binding modes were constructed with three histidines (His(6), His(13), and His(14)), and Asp(1)/Glu(11) of Aβ40 coordinated to Zn(2+). Results from molecular dynamics simulations reveal that the conformational ensembles of different Zn(2+)-Aβ40 complexes are nonoverlapping. The formation of turn structure and, especially, the salt bridge between Glu(22)/Asp(23) and Lys(28) is dependent on specific Zn(2+) binding mode. Agreement with available NMR observations of secondary and tertiary structures could be better achieved if the two simulation results are considered together. The free energy landscape constructed by combining both conformations of Aβ40 indicates that transitions between distinct Aβ40 conformations thar are ready for Zn(2+) binding could be possible in aqueous solution. Markov state model analyses reveal the complex network of conformational space of Aβ40 modeulated by Zn(2+) binding, suggesting various misfolding pathways. The binding free energies evaluated using a combination of quantum mechanics calculations and the MM/3D-RISM method suggest that Glu(11) is the preferred oxygen ligand of Zn(2+). However, such preference is dependent on the relative populations of different conformations with specific Zn(2+) binding modes, and therefore could be shifted when experimental or simulation conditions are altered.

The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine

The environment of sulfur in dissolved aqueous L-cysteine has been examined using K-edge x-ray absorption spectroscopy (XAS), extended continuum multiple scattering (ECMS) theory, and density functional theory (DFT). For the first time, bound-state and continuum transitions representing the entire XAS spectrum of L-cysteine sulfur are accurately reproduced by theory. Sulfur K-edge absorption features at 2473.3 eV and 2474.2 eV represent transitions to LUMOs that are mixtures of S-C and S-H σ∗ orbitals significantly delocalized over the entire L-cysteine molecule. Continuum features at 2479, 2489, and 2530 eV were successfully reproduced using extended continuum theory. The full L-cysteine sulfur K-edge XAS spectrum could not be reproduced without addition of a water-sulfur hydrogen bond. Density functional theory analysis shows that although the Cys(H)S⋯H-OH hydrogen bond is weak (∼2 kcal) the atomic charge on sulfur is significantly affected by this water. MXAN analysis of hydrogen-bonding structures for L-cysteine and water yielded a best fit model featuring a tandem of two water molecules, 2.9 Å and 5.8 Å from sulfur. The model included a S(cys)⋯H-O(w1)H hydrogen-bond of 2.19 Å and of 2.16 Å for H(2)O(w1)⋯H-O(w2)H. One hydrogen-bonding water-sulfur interaction alone was insufficient to fully describe the continuum XAS spectrum. However, density functional theoretical results are convincing that the water-sulfur interaction is weak and should be only transient in water solution. The durable water-sulfur hydrogen bond in aqueous L-cysteine reported here therefore represents a break with theoretical studies indicating its absence. Reconciling the apparent disparity between theory and result remains the continuing challenge.

Modeling copper binding to the amyloid-β peptide at different pH: toward a molecular mechanism for Cu reduction

Oxidative stress, including the production of reactive oxygen species (ROS), has been reported to be a key event in the etiology of Alzheimer's disease (AD). Cu has been found in high concentrations in amyloid plaques, a hallmark of AD, where it is bound to the main constituent amyloid-β (Aβ) peptide. Whereas it has been proposed that Cu-Aβ complexes catalyze the production of ROS via redox-cycling between the Cu(I) and Cu(II) state, the redox chemistry of Cu-Aβ and the precise mechanism of redox reactions are still unclear. Because experiments indicate different coordination environments for Cu(II) and Cu(I), it is expected that the electron is not transferred between Cu-Aβ and reactants in a straightforward manner but involves structural rearrangement. In this work the structures indicated by experimental data are modeled at the level of modern density-functional theory approximations. Possible pathways for Cu(II) reduction in different coordination sites are investigated by means of first-principles molecular dynamics simulations in the water solvent and at room temperature. The models of the ligand reorganization around Cu allow the proposal of a preferential mechanism for Cu-Aβ complex reduction at physiological pH. Models reveal that for efficient reduction the deprotonated amide N in the Ala 2-Glu 3 peptide bond has to be protonated and that interactions in the second coordination sphere make important contributions to the reductive pathway, in particular the interaction between COO(-) and NH(2) groups of Asp 1. The proposed mechanism is an important step forward to a clear understanding of the redox chemistry of Cu-Aβ, a difficult task for spectroscopic approaches as the Cu-peptide interactions are weak and dynamical in nature.

Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules

The pathogenesis of Alzheimer's disease (AD) has been suggested to be related with the aggregation of amyloid β (Aβ) peptides. Metal ions (e.g. Cu, Fe, and Zn) are supposed to induce the aggregation of Aβ. Recent development of bifunctional molecules that are capable of interacting with Aβ and chelating biometal ions provides promising therapeutics to AD. However, the molecular mechanism for how Aβ, metal ions, and bifunctional molecules interact with each other is still elusive. In this study, the binding mode of Zn(2+)-bound Aβ with bifunctional molecules was investigated by the combination of conformational sampling of full-length Aβ peptides using replica exchange molecular dynamics simulations (REMD) and conformational selection using molecular docking and classical MD simulations. We demonstrate that Zn(2+)-bound Aβ((1-40)) and Aβ((1-42)) exhibit different conformational ensemble. Both Aβ peptides can adopt various conformations to recognize typical bifunctional molecules with different binding affinities. The bifunctional molecules exhibit their dual functions by first preferentially interfering with hydrophobic residues 17-21 and/or 30-35 of Zn(2+)-bound Aβ. Additional interactions with residues surrounding Zn(2+) could possibly disrupt interactions between Zn(2+) and Aβ, which then facilitate these small molecules to chelate Zn(2+). The binding free energy calculations further demonstrate that the association of Aβ with bifunctional molecules is driven by enthalpy. Our results provide a feasible approach to understand the recognition mechanism of disordered proteins with small molecules, which could be helpful to the design of novel AD drugs.

Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics

Binding of divalent metal ions with intrinsically disordered fibrillogenic proteins, such as amyloid-β (Aβ), influences the aggregation process and the severity of neurodegenerative diseases. The Aβ monomers and oligomers are the building blocks of the aggregates. In this work, we report the structures and free energy landscapes of the monomeric zinc(II)-bound Aβ40 (Zn:Aβ40) and zinc(II)-bound Aβ42 (Zn:Aβ42) intrinsically disordered fibrillogenic metallopeptides in an aqueous solution by utilizing an approach that employs first principles calculations and parallel tempering molecular dynamics simulations. The structural and thermodynamic properties, including the secondary and tertiary structures and conformational Gibbs free energies of these intrinsically disordered metallopeptide alloforms, are presented. The results show distinct differing characteristics for these metallopeptides. For example, prominent β-sheet formation in the N-terminal region (Asp1, Arg5, and Tyr10) of Zn:Aβ40 is significantly decreased or lacking in Zn:Aβ42. Our findings indicate that blocking multiple reactive residues forming abundant β-sheet structure located in the central hydrophobic core and C-terminal regions of Zn:Aβ42 via antibodies or small organic molecules might help to reduce the aggregation of Zn(II)-bound Aβ42. Furthermore, we find that helix formation increases but β-sheet formation decreases in the C-terminal region upon Zn(II) binding to Aβ. This depressed β-sheet formation in the C-terminal region (Gly33-Gly38) in monomeric Zn:Aβ42 might be linked to the formation of amorphous instead of fibrillar aggregates of Zn:Aβ42.

NMR solution structure of rat aβ(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease

In an attempt to reveal the mechanism of rats' resistance to Alzheimer's disease, we determined the structure of the metal-binding domain 1-16 of rat β-amyloid (rat Aβ(1-16)) in solution in the absence and presence of zinc ions. A zinc-induced dimerization of the domain was detected. The zinc coordination site was found to involve residues His-6 and His-14 of both peptide chains. We used experimental restraints obtained from analyses of NMR and isothermal titration calorimetry data to perform structure calculations. The calculations employed an explicit water environment and a simulated annealing molecular-dynamics protocol followed by quantum-mechanical/molecular-mechanical optimization. We found that the C-tails of the two polypeptide chains of the rat Aβ(1-16) dimer are oriented in opposite directions to each other, which hinders the assembly of rat Aβ dimers into oligomeric aggregates. Thus, the differences in the structure of zinc-binding sites of human and rat Aβ(1-16), their ability to form regular cross-monomer bonds, and the orientation of their hydrophobic C-tails could be responsible for the resistance of rats to Alzheimer's disease.

Substantial contribution of the two imidazole rings of the His13-His14 dyad to Cu(II) binding in amyloid-β(1-16) at physiological pH and its significance

The interaction of amyloid-β (Aβ) peptide with Cu(II) appears to play an important role in the etiology of Alzheimer's disease. At physiological pH, the Cu(II) coordination in Aβ is heterogeneous, and there exist at least two binding modes in which Cu(II) is coordinated by histidine residues. Electron spin resonance studies have revealed a picture of the Cu(II) binding at a higher or lower pH, where only one of the two binding modes is almost exclusively present. We describe a procedure to directly examine the coordination of Cu(II) to each histidine residue in the dominant binding mode at physiological pH. We use nonlabeled and residue-specifically (15)N-labeled Aβ(1-16). For quantitative analysis, the intensities of three-pulse electron spin-echo envelope modulation (ESEEM) spectra are analyzed. Spectral simulations show that ESEEM intensities provide information about the contribution of each histidine residue. Indeed, the ESEEM experiments at pH 6.0 confirm the dominant contribution of His6 to the Cu(II) coordination as expected from the work of other researchers. Interestingly, however, the ESEEM data obtained at pH 7.4 reveal that the contributions of the three residues to the Cu(II) coordination are in the order of His14 ≈ His6 > His13 in the dominant binding mode. The order indicates a significant contribution from the simultaneous coordination by His13 and His14 at physiological pH, which has been underappreciated. These findings are supported by hyperfine sublevel correlation spectroscopy experiments. The simultaneous coordination by the two adjacent residues is likely to be present in a non-β-sheet structure. The coexistence of different secondary structures is possibly the molecular origin for the formation of amorphous aggregates rather than fibrils at relatively high concentrations of Cu(II). Through our approach, precise and useful information about Cu(II) binding in Aβ(1-16) at physiological pH is obtained without any side-chain modification, amino acid residue replacement, or pH change, each of which might lead to an alteration in the peptide structure or the coordination environment.

Minimal Zn(2+) binding site of amyloid-β

Zinc-induced aggregation of amyloid-β peptide (Aβ) is a hallmark molecular feature of Alzheimer's disease. Here we provide direct thermodynamic evidence that elucidates the role of the Aβ region 6-14 as the minimal Zn(2+) binding site wherein the ion is coordinated by His(6), Glu(11), His(13), and His(14). With the help of isothermal titration calorimetry and quantum mechanics/molecular mechanics simulations, the region 11-14 was determined as the primary zinc recognition site and considered an important drug-target candidate to prevent Zn(2+)-induced aggregation of Aβ.

Competition between histamine-like and poly-imidazole coordination sites for Cu(2+) and Zn(2+) ions in zebra-fish peptide of prion-like protein

The fragment of the zebrafish prion-like protein (PrP-rel-2), encompassing residues 74-86 and unprotected at N-terminus (zf74-86) represents a good model to understand Cu(2+) and Zn(2+) binding to ligands containing multi-potential metal donor sites. Zf(74-86) contains four His and His-1 N-terminal amine groups which constitute both copper and zinc anchoring sites. The presence of His at the first position additionally provides the histamine-like binding mode which could compete with the multi-His binding mode. In this study the speciation profiles of the Cu(2+) and Zn(2+) complexes with zf74-86 have been obtained. The main species, dominating at physiological pH, have been fully characterized by using different spectroscopic techniques. The detected NMR chemical shift variations and line broadening enhancements, caused by Zn(2+) and Cu(2+) respectively, allowed to determine the metal binding sites. Both metal ions showed common binding donor atoms, being 2 or 3 His imidazoles and the N-terminal group involved in Cu(2+) and Zn(2+) binding.