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In this work, the graphene/α-SiO2(0001) interface is calculated using density functional theory. On the oxygen-terminated SiO2 surface, atomic structure reconstruction occurs at the graphene/SiO2 interface to eliminate the dangling bonds. The interface interaction is 77 meV/C atom, which indicates that van der Waals force dominates the interaction, but it is stronger than the force between the graphene layers in graphite. The distance between graphene and the SiO2 surface is 2.805 Å, which is smaller than the 3.4 Å interlayer distance of graphite. In addition, the SiO2 substrate induces p-type doping in graphene and opens a small gap of 0.13 eV at the Dirac point of graphene, which is desirable for electronic device applications.

Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e1 bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

Peptide amphiphile (PA) molecules that self-assemble in vivo into supramolecular nanofibers were used as a therapy in a mouse model of spinal cord injury (SCI). Because self-assembly of these molecules is triggered by the ionic strength of the in vivo environment, nanoscale structures can be created within the extracellular spaces of the spinal cord by simply injecting a liquid. The molecules are designed to form cylindrical nanofibers that display to cells in the spinal cord the laminin epitope IKVAV at nearly van der Waals density. IKVAV PA nanofibers are known to inhibit glial differentiation of cultured neural stem cells and to promote neurite outgrowth from cultured neurons.In this work, in vivo treatment with the PA after SCI reduced astrogliosis, reduced cell death, and increased the number of oligodendroglia at the site of injury. Furthermore, the nanofibers promoted regeneration of both descending motor fibers and ascending sensory fibers through the lesion site.Treatment with the PA also resulted in significant behavioral improvement. These observations demonstrate that it is possible to inhibit glial scar formation and to facilitate regeneration after SCI using bioactive three-dimensional nanostructures displaying high densities of neuroactive epitopes on their surfaces.

Aggregation of amyloid-β peptides (Aβ) into fibrils is the key pathological feature of many neurodegenerative disorders. Typical drugs inhibit Aβ fibrillation by binding to monomers in 1:1 ratio and display low efficacy. Here, we report that model CdTe nanoparticles (NPs) can efficiently prevent fibrillation of Aβ associating with 100–330 monomers at once. The inhibition is based on the binding multiple Aβ oligomers rather than individual monomers. The oligomer route of inhibition is associated with strong van der Waals interactions characteristic for NPs and presents substantial advantages in the mitigation of toxicity of the misfolded peptides. Molar efficiency and the inhibition mechanism revealed by NPs are analogous to those found for proteins responsible for prevention of amyloid fibrillation in human body. Besides providing a stimulus for finding biocompatible NPs with similar capabilities, these data suggest that inorganic NPs can mimic some sophisticated biological functionalities of proteins.

Collagen type I fibrils are the major building blocks of connective tissues. Collagen fibrils are anisotropic supra-molecular structures, and their orientation can be revealed by polarized light microscopy and vibrational microspectroscopy. We hypothesized that the anisotropy of chemical bonds in the collagen molecules, and hence their orientation, might also be detected by X-ray photoemission electron spectromicroscopy (X-PEEM) and X-ray absorption near-edge structure (XANES) spectroscopy, which use linearly polarized synchrotron light. To test this hypothesis, we analyzed sections of rat-tail tendon, composed of parallel arrays of collagen fibrils. The results clearly indicate that XANES-PEEM is sensitive to collagen fibril orientation and, more specifically, to the orientations of carbonyl and amide bonds in collagen molecules. These data suggest that XANES-PEEM is a promising technique for characterizing the chemical composition and structural organization at the nanoscale of collagen-based connective tissues, including tendons, cartilage, and bone.

β-2-microglobulin (β2m) deposits as amyloid fibrils in the musculoskeletal system of patients undergoing long-term dialysis treatment as a result of kidney failure. Previous work has shown that Cu(II) binding causes β2m to organize into native-like dimers and tetramers that precede amyloid formation. Cu(II) is then released from higher order oligomers before mature Cu(II)-free amyloid fibrils are formed. While some of the Cu(II)-induced structural changes that enable β2m self assembly are starting to be revealed, the details of how the Cu(II) binding site evolves from the monomer to the dimers and tetramers are not known. Here, we report results from three mass spectrometry (MS) based methods that provide insight into the changing Cu-β2m interactions. We find that monomeric β2m binds Cu(II) via the N-terminal amine, the amide of Gln2, His31, and Asp59. In the dimer and tetramer, Asp59 is no longer bound to Cu(II), but the other residues still comprise a well-defined albeit weaker binding site that is better able to release Cu(II). Consistent with this is the observation that a fraction of the tetrameric species no longer binds Cu(II) at this weakened binding site, which agrees with a previous report that suggested the tetramer as the first Cu(II)-free oligomer. Our results also provide some insight into structural changes caused by Cu(II) binding that facilitate oligomer formation. Specifically, binding by Asp59 in the monomer requires significant movement of this residue, and we propose that this repositioning is important for establishing a pair of dimer-stabilizing salt bridges between this residue and Lys19. We also find evidence that Cu(II) binding in the N-terminal region of the monomer repels Arg3, which likely allows this residue to form a pair of dimer-stabilizing salt bridges with Glu16. Overall, our measurements suggest that the previously proposed conformational switch caused by Cu(II) binding includes not only a cis-trans isomerization at Pro32 but also the repositioning of residues that are critical for the formation of new electrostatic interactions.

Summary

β2-microglobulin (β2m) is the light chain of type I major histocompatibility complex. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. Despite the devastating effects of dialysis-related amyloidosis, full understanding of how fibrils form from soluble β2m remains elusive. Here we show that β2m can oligomerize and fibrillize via 3D domain swapping. Isolating a covalently bound, domain-swapped dimer from β2m oligomers on the pathway to fibrils, we were able to determine its crystal structure. The hinge loop which connects the swapped domain to the core domain includes the fibrillizing segment LSFSKD, whose atomic structure we also determined. The LSFSKD structure reveals a Class 5 steric zipper, akin to other amyloid spines. The structures of the dimer and the zipper spine fit well into an atomic model for this fibrillar form of β2m, which assembles slowly under physiological conditions.

Background

Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation.

Methods and Findings

Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR.

Conclusions

Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils.

The title compound, [Fe(C5H5)(C18H15N2O)], a product of the reaction of 2-ferrocenylbenzoic acid and 2-amino-6-methyl­pyridine, crystallizes with two dissimilar mol­ecules in the asymmetric unit. In one mol­ecule, the picoline amide group is directed away from the 2-ferrocenylbenzene moiety (anti) whereas in the other, these are proximate (syn). In the crystal structure, mol­ecules aggregate into dimers via cyclic, asymmetric N—H⋯N inter­actions with graph set R 2 2(8), and are further augmented via intra­molecular C—H⋯O=C and inter­dimer C—H⋯π(arene) inter­actions. Dimers are linked into chains along the [102] direction via weak C—H⋯O hydrogen bonds.

The title compound, C17H18N2OS, adopts a trans–cis geometry of the thio­urea group which is stabilized by intra­molecular hydrogen bonds between the O atom of the carbonyl group and the H atom of the thio­amide group. A C—H⋯S intramolecular hydrogen bond is also present. In the crystal structure, mol­ecules are linked by inter­molecular N—H⋯S hydrogen bonds to form centrosymmetric dimers.

The Cd atom in the title compound, [Cd(C12H10N2O)3](NO3)2, adopts a distorted octa­hedral geometry, being ligated by six N atoms from three different phenyl-2-pyridyl ketone oxime ligands. In the crystal structure, inter­molecular O—H⋯O and C—H⋯O hydrogen bonds link the mol­ecules into a chain structure propagating along [100]. The chains are further linked into a three-dimensional supra­molecular structure via van der Waals forces.

The title compound, C12H8F2N2O, crystallizes with two independent mol­ecules in the asymmetric unit. The independent mol­ecules differ slightly in conformation; the dihedral angles between the benzene and pyridine rings are 51.58 (5) and 49.97 (4)°. In the crystal structure, mol­ecules aggregate via N—H⋯Npyridine inter­actions as hydrogen-bonded dimers with the structural motif R 2 2(8), and these dimers are linked via C—H⋯O inter­actions to form a supra­molecular chain.

In the structure of the title compound, [Li(C5H4N2O2)(NO3)]n, the LiI ion is coordinated by two carboxyl­ate O atoms donated by two ligands and two nitrate O atoms in a distorted tetrahedral geometry. LiI ions, bridged by carboxyl­ate O atoms, form mol­ecular ribbons composed of dimeric units. Two nitrate O atoms link the ribbons into mol­ecular layers parallel to (001). Hydrogen bonds are active between protonated heterocyclic N atoms as donors and carboxyl­ate O atoms as acceptors. The layers are held together by van der Waals inter­actions.

The title benzyl Grignard reagent, [Mg2Br2(C7H7)2(C4H10O)2], was obtained by reaction of benzyl bromide with magnesium in diethyl ether, followed by crystallization from toluene. The asymmetric unit comprises one half-mol­ecule, the structural dimeric unit being generated by inversion symmetry with an Mg⋯Mg distance of 3.469 (2) Å. The Mg(II) atom exhibits a distorted tetrahedral coordination geometry. The crystal packing is defined by van der Waals inter­actions only.

The benzene ring in the title compound, C10H10O4, makes an angle of 4.4 (1)° with the C—C—C—O linker. The hy­droxy groups are involved in both intra- and inter­molecular O—H⋯O hydrogen bonds. The crystal packing is stabilized by O—H⋯O hydrogen-bonding inter­actions. The mol­ecules of the caffeic acid ester form a dimeric structure in a head-to-head manner along the a axis through O—H⋯O hydrogen bonds. The dimers inter­act with one another through O—H⋯O hydrogen bonds, forming supermolecular chains. These chains are further extended through C—H⋯O hydrogen bonds as well as van der Waals inter­actions into the final three-dimensional architecture.

The title compound, C21H28N2O5, has two intra­molecular N—H⋯O hydrogen bonds. Inter­molecular N—H⋯O hydrogen bonds [graph-set motif R 2 2(8)] give rise to a dimer. Weak N—H⋯N hydrogen bonds between neighboring dimers further extend the crystal structure, which exhibits an infinite chain motif.

The title complex, (C5H7N2)[PbI3], consists of a 1-amino­pyridinium cation, disordered about a mirror plane, and a [PbI3]− anion. The Pb2+ ion (site symmetry ) is surrounded by six I atoms in a slightly distorted octa­hedral coordination. The PbI6 octa­hedra share faces, building up ∞ 1[PbI6/2] chains running along [010]. The cations are situated between the chains. Coulombic attractions and van der Waals inter­actions between the inorganic and organic components are mainly responsible for the cohesion of the structure.

Summary

Amyloid diseases are characterized by the misfolding of a precursor protein that leads to amyloid fibril formation. Despite the fact that there are different precursors, some commonalities in the misfolding mechanism are thought to exist. In light chain amyloidosis (AL), the immunoglobulin light chain (LC) forms amyloid fibrils that deposit in the extracellular space of vital organs. AL proteins are thermodynamically destabilized compared to non-amyloidogenic proteins and some studies have linked this instability to increased fibril formation rates. Here we present the crystal structures of two highly homologous AL proteins, AL-12 and AL-103. This structural study shows that these proteins retain the canonical germline dimer interface. We highlight important structural alterations in two loops flanking the dimer interface and correlate these results with the somatic mutations present in AL-12 and AL-103. We suggest that these alterations are informative structural features that are likely contributing to protein instability that leads to conformational changes involved in the initial events of amyloid formation.

The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.

Experimental evidence suggests that a tetramer of integrase (IN) is the protagonist of the concerted strand transfer reaction, whereby both ends of retroviral DNA are inserted into a host cell chromosome. Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visna virus IN in complex with the IN binding domain of the common lentiviral integration co-factor LEDGF. The structures reveal that the dimer-of-dimers architecture of the IN tetramer is stabilized by swapping N-terminal domains between the inner pair of monomers poised to execute catalytic function. Comparison of four independent IN tetramers in our crystal structures elucidate the basis for the closure of the highly flexible dimer-dimer interface, allowing us to model how a pair of active sites become situated for concerted integration. Using a range of complementary approaches, we demonstrate that the dimer-dimer interface is essential for HIV-1 IN tetramerization, concerted integration in vitro, and virus infectivity. Our structures moreover highlight adaptable changes at the interfaces of individual IN dimers that allow divergent lentiviruses to utilize a highly-conserved, common integration co-factor.

Author Summary

Integrase is the viral enzyme that orchestrates insertion of both ends of retroviral DNA into a host cell chromosome. This process, thought to require a tetramer of integrase, involves two concerted cutting/joining (transesterification) reactions that target a pair of phosphodiester bonds in chromosomal DNA, separated by ∼18 Å. Until now, the architecture of the integrase tetramer responsible for concerted integration has remained a mystery. We now report two crystal structures containing the N-terminal and catalytic core domains from a lentiviral integrase in complex with its co-factor LEDGF. Comparison of the structural arrangements observed in our crystals elucidates the details of the integrase tetramerization interface, reveals its dramatic flexibility and the mechanism by which a pair of active sites can be brought into close proximity. Taking advantage of the structural data, we generated a series of HIV-1 integrase mutants designed to disrupt or re-create its tetramerization interface. Biochemical and virus replication studies with these mutants strongly support the functional significance of the tetrameric architecture observed in the crystal structures. Our results provide important novel insights into the assembly of the functional integrase tetramer and will be invaluable for the ongoing efforts to model the retroviral pre-integration complex.

The main pathogenic process underlying dialysis-related amyloidosis (DRA) is the accumulation of β-2-microglobulin (β2m) as amyloid fibrils in the musculoskeletal system, and some evidence suggests that Cu(II) may play a role in β2m amyloid formation. Cu(II)-induced β2m fibril formation is preceded by the formation of discrete, oligomeric intermediates, including dimers, tetramers, and hexamers. In this work, we use selective covalent labeling reactions combined with mass spectrometry to investigate the amino acids responsible for mediating tetramer formation in wild-type β2m. By comparing the labeling patterns of the monomer, dimer, and tetramer, we find evidence that the tetramer interface is formed by the interaction of D strands from one dimer unit and G strands from another dimer unit. This covalent labeling data along with molecular dynamics calculations enable the construction of a tetramer model that indicates how the protein might proceed to form even higher order oligomers.

The treatment of van der Waals interactions in density functional theory is an important field of ongoing research. Among different approaches developed recently to capture these non-local interactions, the van der Waals density functional (vdW-DF) developed in the groups of Langreth and Lundqvist is becoming increasingly popular. It does not rely on empirical parameters, and has been successfully applied to molecules, surface systems, and weakly-bound solids. As the vdW-DF requires the evaluation of a six-dimensional integral, it scales, however, unfavorably with system size. In this work, we present a numerically efficient implementation based on the Monte-Carlo technique for multi-dimensional integration. It can handle different versions of vdW-DF. Applications range from simple dimers to complex structures such as molecular crystals and organic molecules physisorbed on metal surfaces.

Highlights

► We present a numerically efficient implementation of van der Waals DFT. ► The computational efficiency is achieved through the usage of the Monte-Carlo integration technique. ► It scales particularly well for periodic systems. ► The code can be used on top of any DFT code. ► Different flavors of vdW density functionals are included.

Recent experiments have shown that the congener, Aβ1–40[D23-K28], in which the side chains of charged residues Asp23 and Lys28 are linked by a lactam bridge, forms amyloid fibrils that are structurally similar to the wild type (WT) Aβ peptide, but at a rate that is nearly thousand times faster. We used all atom molecular dynamics in explicit water, and two force fields, of the WT dimer, a monomer with the lactam bridge (Aβ10–35-lactam[D23-K28]), the monomer and dimers with harmonically constrained D23-K28 salt bridge (Aβ10–35[D23-K28]), to understand the origin of the enhanced fibril rate formation. The simulations show that the assembly-competent fibril like monomer (N*) structure, that is present among the conformations sampled by the isolated monomer, with strand conformations in the residues spanning the N and C termini and a bend involving residues D23VGSNKG29, are populated to a much greater extent in Aβ10–35[D23-K28] and Aβ10–35-lactam[D23-K28] than in the WT, which has negligible probability of forming N*. The salt bridge in N* of Aβ10–35[D23-K28], whose topology is similar to that found in the fibril, is hydrated. The reduction in the free energy barrier to fibril formation in Aβ10–35[D23-K28] and in Aβ10–35-lactam[D23-K28], compared to the WT, arises largely due to entropic restriction that enables the bend formation. A decrease in the entropy of the unfolded state and the lesser penalty for conformational rearrangement including the formation of the salt bridge in Aβ peptides with D23-K28 constraint results in a reduction in the kinetic barrier in the Aβ1–40-lactam[D23-K28] congener compared to the WT. The decrease in the barrier, that is related to the free energy cost of forming a bend, is estimated to be in the range (4–7)kBT. Although a number of factors determine the growth of fibrils, the decrease in the free energy barrier, relative to the WT, to N* formation is a major factor in the rate enhancement in the fibril formation of Aβ1–40[D23-K28] congener. Qualitatively similar results were obtained using simulations of Aβ9–40 peptides, and various constructs related to the Aβ10–35 systems that were probed using OPLS and CHARMM force fields. We hypothesize that mutations or other constraints that preferentially enhance the population of N* species would speed up aggregation rates. Conversely, ligands that lock it in the fibril-like N* structure would prevent amyloid formation.

Summary

Light chain amyloidosis is a devastating protein misfolding disease characterized by the accumulation of amyloid fibrils that causes tissue damage and organ failure. These fibrils are composed of monoclonal light chain protein secreted from an abnormal proliferation of bone marrow plasma cells. We previously reported that amyloidogenic light chain protein AL-09 adopts an altered dimer while its germline protein (κI O18/O8) forms a canonical dimer observed in other light chain crystal structures. In solution, conformational heterogeneity obscures all NMR signals at the AL-09 and κI O18/O8 dimer interfaces, so we solved NMR structure of two related mutants. AL-09 H87Y adopts the normal dimer interface, but the κI Y87H solution structure presents an altered interface rotated 180° relative to the canonical dimer interface and 90° from the AL-09 arrangement. Our results suggest promiscuity in the light chain dimer interface may promote new intermolecular contacts that may contribute to amyloid fibril structure.

The mol­ecule of the title Schiff base compound, C10H11N3O2, adopts an E geometry with respect to the C=N double bond. The mol­ecule is roughly planar, with the largest deviation from the mean plane being 0.111 (2) Å, The enyl­idene-hydrazine group is, however, slightly twisted with respect to the phenyl ring, making a dihedral angle of 6.5 (3)°. An intra­molecular N—H⋯O hydrogen bond may be responsible for the planar conformation. An inter­molecular N—H⋯O hydrogen bond links two mol­ecules around an inversion center, building a pseudo dimer.