Tetrameric Aß40 and Aß42 ß-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.

Alzheimer's disease (AD) is characterized by the accumulation of extracellular Aß42 and Aß40 oligomers and plaques. In a recent computational study, we found that the presence of the residues I41 and A42 increases significantly the propensity of Aß to form a tetrameric ß-barrel structure in a bilayer mimicking a neuronal membrane. In this work, we have determined the propensity of the two Aß proteins to form tetrameric ß-barrel structures in aqueous solution using four atomistic protein fields, that is, Amber99SB-ILDN/TIP3P, OPLS/TIP3P, CHARMM36m/TIP3P-modified, and Amber99SB/DISP. Extensive replica exchange molecular dynamics simulations make it clear that a ß-barrel, made of two distinct ß-hairpin motifs and an asymmetric arrangement of eight antiparallel ß-strands with an inner pore diameter of 0.7 nm, exists transiently for Aß42 peptide, but this is less the case for Aß40 peptide, due to the change of the CHC-CHC and the Cter-Cter interfaces. This study has several implications in AD.

Tetrameric Aß40 and Aß42 ß-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.

The amyloid-ß (Aß) 42 oligomers are much more toxic than Aß40 oligomers in Alzheimer's disease. Numerous experiments indicate that toxicity could involve the formation of pores in membranes, but experimental high-resolution structure determination of these pore-forming Aß oligomers has been impeded by aggregate heterogeneity. Using extensive atomistic simulations, low-resolution data obtained in lipid bilayers, and other theoretical factors, we proposed atomic structures of Aß40 and Aß42 ß-barrels in a bilayer mimicking a neuronal membrane. The 3D model, which consists of tetramer subunits, two distinct ß-hairpin motifs and an asymmetric arrangement of eight antiparallel ß-strands, is drastically destabilized for Aß40 compared to its Aß42 counterpart. Our computational modeling has several implications in Alzheimer's disease, sheds light on the amyloid pore hypothesis, and explains the higher deleterious property of Aß42.

Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations.

Lipophilicity is a fundamental property to characterize the structure and function of proteins, motivating the development of lipophilicity scales. We report a versatile strategy to derive a pH-adapted scale that relies on theoretical estimates of distribution coefficients from conformational ensembles of amino acids. This is accomplished by using an accurately parametrized version of the IEFPCM/MST continuum solvation model as an effective way to describe the partitioning between n-octanol and water, in conjunction with a formalism that combines partition coefficients of neutral and ionic species of residues and the corresponding p Ka values of ionizable groups. Two weighting schemes are considered to derive solvent-like and protein-like scales, which have been calibrated by comparison with other experimental scales developed in different chemical/biological environments and pH conditions as well as by examining properties such as the retention time of small peptides and the recognition of antigenic peptides. A straightforward extension to nonstandard residues is enabled by this efficient methodological strategy.

Synthesis and biological properties of aryl methyl sulfones.

A novel group of aryl methyl sulfones based on nonsteroidal anti-inflammatory compounds exhibiting a methyl sulfone instead of the acetic or propionic acid group was designed, synthesized and evaluated in vitro for inhibition against the human cyclooxygenase of COX-1 and COX-2 isoenzymes and in vivo for anti-inflammatory activity using the carrageenan induced rat paw edema model in rats. Also, in vitro chemosensitivity and in vivo analgesic and intestinal side effects were determined for defining the therapeutic and safety profile. Molecular modeling assisted the design of compounds and the interpretation of the experimental results. Biological assay results showed that methyl sulfone compounds 2 and 7 were the most potent COX inhibitors of this series and best than the corresponding carboxylic acids (methyl sulfone 2: IC50 COX-1 = 0.04 and COX-2 = 0.10 µM, and naproxen: IC50 COX-1 = 11.3 and COX-2 = 3.36 µM). Interestingly, the inhibitory activity of compound 2 represents a significant improvement compared to that of the parent carboxylic compound, naproxen. Further support to the results were gained by the docking studies which suggested the ability of compound 2 and 7 to bind into COX enzyme with low binding free energies. The improvement of the activity of some sulfones compared to the carboxylic analogues would be performed through a change of the binding mode or mechanism compared to the standard binding mode displayed by ibuprofen, as disclosed by molecular modeling studies. So, this study paves the way for further attention in investigating the participation of these new compounds in the pain inhibitory mechanisms. The most promising compounds 2 and 7 possess a therapeutical profile that enables their chemical scaffolds to be utilized for development of new NSAIDs.

Prediction of pH-Dependent Hydrophobic Profiles of Small Molecules from Miertus-Scrocco-Tomasi Continuum Solvation Calculations.

Hydrophobicity is a key physicochemical descriptor used to understand the biological profile of (bio)organic compounds as well as a broad variety of biochemical, pharmacological, and toxicological processes. This property is estimated from the partition coefficient between aqueous and nonaqueous environments for neutral compounds (PN) and corrected for the pH-dependence of ionizable compounds as the distribution coefficient (D). Here, we have extended the parametrization of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol to nitrogen-containing heterocyclic compounds, as they are present in many biologically relevant molecules (e.g., purines and pyrimidines bases, amino acids, and drugs), to obtain accurate log PN values for these molecules. This refinement also includes solvation calculations for ionic species in n-octanol with the aim of reproducing the experimental partition of ionic compounds (PI). Finally, the suitability of different formalisms to estimate the distribution coefficient for a wide range of pH values has been examined for a set of small acidic and basic compounds. The results indicate that in general the simple pH-dependence model of the ionizable compound in water suffices to predict the partitioning at or around physiological pH. However, at extreme pH values, where ionic species are predominant, more elaborate models provide a better prediction of the n-octanol/water distribution coefficient, especially for amino acid analogues. Finally, the results also show that these formalisms are better suited to reproduce the experimental pH-dependent distribution curves of log D for both acidic and basic compounds as well as for amino acid analogues.

Dimerization Mechanism of Alzheimer Aß40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation.

Amyloid beta (Aß) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aß40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aß40 dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel ß-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded ß-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded ß-sheet or inhibiting the formation of an interpeptide ß-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of Aß species.

Proline cis-trans isomerization and its implications for the dimerization of analogues of cyclopeptide stylostatin 1: a combined computational and experimental study.

Cis and trans proline conformers are often associated with dramatic changes in the biological function of peptides. A slow equilibrium between cis and trans Ile-Pro amide bond conformers occurs in constrained derivatives of the native marine cyclic heptapeptide stylostatin 1 (cyclo-(NSLAIPF)), a potential anticancer agent. In this work, four cyclopeptides, cyclo-(NSTAIPF), cyclo-(KSTAIPF), cyclo-(RSTAIPF) and cyclo-(DSTAIPF), which are structurally related to stylostatin 1, are experimentally and computationally examined in order to assess the effect of residue mutations on the cis-trans conformational ratio and the apparent capacity to form dimeric aggregates. Primarily, cyclo-(KSTAIPF) and cyclo-(RSTAIPF) showed specific trends in circular dichroism, MALDI-TOF and HPLC purification experiments, which suggests the occurrence of peptide dimerization. Meanwhile, the NMR spectrum of cyclo-(KSTAIPF) indicates that this cyclopeptide exists in the two slow-exchange families of conformations mentioned above. Molecular dynamics simulations combined with quantum mechanical calculations have shed light on the factors governing the cis/trans conformational ratio. In particular, we have found that residue mutations affect the internal hydrogen bond pattern which ultimately tunes the cis/trans conformational ratio and that only trans conformers are capable of aggregating due to the shape complementarity of the two subunits.

Impact of the A2V Mutation on the Heterozygous and Homozygous Aß1-40 Dimer Structures from Atomistic Simulations.

The A2V mutation was reported to protect from Alzheimer's disease in its heterozygous form and cause an early Alzheimer's disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of Aß1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded ß-sheets is increased, and the number of all α dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the Aß1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.

The ortho-substituent effect on the Ag-catalysed decarboxylation of benzoic acids.

A combined experimental and computational investigation on the Ag-catalysed decarboxylation of benzoic acids is reported herein. The present study demonstrates that a substituent at the ortho position exerts dual effects in the decarboxylation event. On one hand, ortho-substituted benzoic acids are inherently destabilised starting materials compared to their meta- and para-substituted counterparts. On the other hand, the presence of an ortho-electron-withdrawing group results in an additional stabilisation of the transition state. The combination of both effects results in an overall reduction of the activation energy barrier associated with the decarboxylation event. Furthermore, the Fujita-Nishioka linear free energy relationship model indicates that steric bulk of the substituent can also exert a negative effect by destabilising the transition state of decarboxylation.

Phospholipid-lactose permease interaction as reported by a head-labeled pyrene phosphatidylethanolamine: a FRET study.

Förster resonance energy transfer (FRET) measurements were performed in preceding works to study the selectivity between a single-tryptophan mutant of lactose permease (LacY) of Escherichia coli (used as the donor) and phospholipid probes labeled with pyrene at the acyl chain moiety (used as the acceptor). In the present work, we report the results obtained by using the same LacY mutant (W151/C154G) and binary lipid mixtures of phosphatidylethanolamine (PE) differing in the acyl chain composition and 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG) (3:1 mol/mol) doped with a phospholipid probe labeled with pyrene at the headgroup. The use of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(1-pyrenesulfonyl) ammonium salt (HPyr-PE), which bears two unsaturated acyl chains, enabled the investigation of the specific interaction between LacY and HPyr-PE. The main conclusions raised from our results suggest that (i) for phase-separated systems, LacY would be located in fluid domains nominally enriched in POPG, and if a given proportion of PE is present in this phase, it will be mainly located around LacY; and (ii) in the absence of phase separation, LacY is preferentially surrounded by PE and, in particular, seems to be sensitive to the lipid spontaneous curvature.

First diastereoselective [3 + 2] cycloaddition reaction of diethyl isocyanomethylphosphonate and maleimides.

Bicyclic α-iminophosphonates were prepared via the first diastereoselective silver catalyzed [3 + 2] cycloaddition reaction of diethyl isocyanomethylphosphonate and diversely N-substituted maleimides. The reduction of the resulting imine by catalytic hydrogenation led to cyclic α-aminophosphonates, which are α-aminoester surrogates. The relative stereochemistry of the adducts was confirmed by X-ray crystallographic analysis of . The diastereoselectivity of the cycloaddition reaction was rationalised by theoretical studies.

Allosteric regulation of PKCθ: understanding multistep phosphorylation and priming by ligands in AGC kinases.

Protein kinases play critical roles in cellular activation and differentiation, and are involved in numerous pathophysiological processes. As a critical component of the regulatory circuitry of the cell, the kinase domain has the ability to integrate multiple signals, yielding a predetermined output. In PKC and other protein kinases of the AGC family, several phosphorylation sites control the activity, but these are in turn influenced by the presence of ligands in the binding pocket, which promotes phosphorylation. Here, we take PKC-theta as a prototypical member of the family and use molecular dynamics simulations to investigate the cross-talk that exists between regulatory and functional sites. We first show how the apo-unphosphorylated form of the kinase is populating a conformational space in which access to the ATP binding site and to the activation loop (AL) are simultaneously hindered. This could explain why the inactive state is not only catalytically incompetent but also resistant to activation. AL phosphorylation induces ATP binding site opening, which can then readily accept the cofactor. But the signal transmission mechanism works both ways, and if ligand binding to the unphosphorylated form occurs first, the AL is de-protected and becomes exposed to phosphorylation, thus providing an explanation for the paradoxical activation of PKCs by their inhibitors.

MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Abeta(10-35)) aggregation.

Recent experiments with amyloid-beta (Abeta) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Abeta(10-35) monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

Chemical reactivity of D3h C78 (metallo)fullerene: regioselectivity changes induced by Sc3N encapsulation.

We report here for the first time a full comparison of the exohedral reactivity of a given fullerene and its parent trinitride template endohedral metallofullerene. In particular, we study the thermodynamics and kinetics for the Diels-Alder [4 + 2] cycloaddition between 1,3-butadiene and free D3h'-C78 fullerene and between butadiene and the corresponding endohedral D3h-Sc3N@C78 derivative. The reaction is studied for all nonequivalent bonds, in both the free and the endohedral fullerenes, at the BP86/TZP//BP86/DZP level. The change in exohedral reactivity and regioselectivity when a metal cluster is encapsulated inside the cage is profound. Consequently, the Diels-Alder reaction over the free fullerene and the endohedral derivative leads to totally different cycloadducts. This is caused by the metal nitride situated inside the fullerene cage that reduces the reactivity of the free fullerene and favors the reaction over different bonds.

Combined theoretical and experimental analysis of the bonding in the heterobimetallic cubane-type Mo(3)NiS(4) and Mo(3)CuS(4) core clusters.

X-ray structural data for the cubane-type clusters [Mo3CuS4(dmpe)3Cl4](+) and Mo3NiS4(dmpe)3Cl4 (dmpe = 1,2-bis(dimethylphosphino)ethane) with 16 metal electrons have been compared with optimized structural parameters calculated using "ab initio" methodologies. Compound Mo3NiS4(dmpe)3Cl4 crystallizes in the cubic noncentrosymmetric space group P213 with a Mo-Ni distance of 2.647 Angstrom, that is 0.2 Angstrom shorter than the Mo-Cu bond length in the isoelectronic copper cluster. The best agreement between theory and experiments has been obtained using the B3P86 method. In order to validate the B3P86 results, accurate infrared and Raman spectra have been acquired and the vibrational modes associated to the cubane-type Mo3M'S4 (M' = Cu or Ni) unit have been assigned theoretically. The electronic changes taking place when incorporating the M' into the Mo3S4 unit have been analyzed from a theoretical and experimental perspective. The bond dissociation energies between M'-Cl and Mo3S4 fragments show that formation of [Mo3CuS4(dmpe)3Cl4](+) is 135 kcal/mol energetically less favorable than the Ni incorporation. The more robust nature of the Mo3NiS4 fragment has been confirmed by mass spectrometry. The X-ray photoelectron spectroscopy (XPS) spectra of the trimetallic and tetrametallic complexes have been measured and the obtained binding energies compared with the computed electronic populations based on topological approaches of the electron localization function (ELF). The energies and shapes of the Cu 2p and Ni 2p lines indicate formal oxidation states of Cu(I) and Ni(II). However, the reductive addition of nickel into [Mo3S4(dmpe)3Cl3](+) causes a small decrease in the Mo 3d binding energies. This fact prevents an unambiguous assignment of an oxidation state in a conventional way, a circumstance that has been analyzed through the covariance of the electronic populations associated to the C(M') core and V(Mo3Ni) and V(S(2)') valence basins where Mo3NiS4 is a particularly electronically delocalized chemical entity.

Exohedral reactivity of trimetallic nitride template (TNT) endohedral metallofullerenes.

[structures: see text] Fullerenes containing a trimetallic nitride template (TNT) within the cage are a particularly interesting class of endohedral metallofullerenes. Recently two exohedral derivatives of the Sc3N@C80 fullerene have been synthesized: a Diels-Alder and a fulleropyrrolidine cycloadduct. The successful isolation, purification, and structural elucidation of these metallofullerenes derivatives have encouraged us to understand how the chemical reactivity is affected by TNT encapsulation. First of all, we predicted the most reactive exohedral sites, taking into account the double bond character and the pyramidalization angle of the C-C bonds. For this purpose, a full characterization of all different types of C-C bonds of the following fullerenes was carried out: I(h)-C60:1, D3-C68:6140, D3-Sc3N@C68, D(5h)-C70:1, D(3h')-C78:5, D(3h)-Sc3N@C78, I(h)-C80:7 and several isomers of Sc3N@C80. Finally the exohedral reactivity of these TNT endohedral metallofullerenes, via [4 + 2] cycloaddition reactions of 1,3-butadiene, was corroborated by means of DFT calculations.

Prediction of heterofullerene stabilities: a combined DFT and chemometric study of C56Pt2, C57Pt2 and C81Pt2.

A systematic search of the regioisomers of the heterofullerenes, C57Pt2 and C56Pt2, has been carried out by means of density functional calculations to find the most stable structures. Both heterofullerenes incorporate two metal atoms into the fullerene surface. In the case of C57Pt2, one platinum atom substitutes one carbon atom of C60 and the other platinum atom replaces a C--C bond, whereas in C56Pt2 each platinum atom replaces one C--C bond. Several geometric factors were studied, three of which have particularly important effects on the relative stabilities of the regioisomers: the Pt--Pt separation, the number of C--C bonds remaining after substitution, and the type of C--C bond that is substituted. All these factors indicate that the deformation of the carbon framework is a general factor that governs the relative stabilities of the regioisomers. Because a high number of factors affect the stability of the heterofullerenes we also used chemometric techniques in this study. Partial least-squares (PLS) regression was used to establish the structure-energy relationships of C57Pt2 and C56Pt2 heterofullerenes. The understanding gained of the factors that affect the relative isomers stabilities has allowed us to predict the stabilities of larger disubstituted carbon cages, for example, C81Pt2 heterofullerene.

Analysis of polyaddition levels in i-Sc3NC80.

Using the density functional method, the stabilities of highly hydrogenated and fluorinated [80]fullerenes, both empty and containing the Sc3N molecule, have been calculated. Addition of 44 atoms to i-Sc3NC80 is predicted to be most favorable due to the formation of six octahedrally located benzenoid rings, while addition of up to 52 atoms (consistent with preliminary fluorination data) gives a structure stabilized by the presence of four benzenoid rings. The most stable isomers at this addition level have been determined and the relative stabilities of a number of C80H52, C80F52, and i-Sc3NC80H52 species calculated. The hydrogenation of the i-Sc3NC80 has been computed to be more difficult than the corresponding partner, C80. From the geometrical point of view, the Sc3N molecule is planar in the parent [80]fullerene but is calculated to be pyramidal in some of the hydrogenated/fluorinated derivatives. Moreover, in these it has fixed locations due to orbital interactions arising from deformation of the cage and the presence of localized double bonds.